New Crocodile Species Found in Mexico

QUINTANA ROO, Mexico — A study has revealed that the crocodiles of Cozumel and Banco Chinchorro, in the state of Quintana Roo, conceal distinct lineages that could constitute two new species. These island populations show unique adaptations: in Cozumel, smaller clutches and longer snouts for catching fish; in Chinchorro, tolerance to extreme salinity and wider skulls for breaking shells.

Genetic analyses indicate that both populations separated from the mainland approximately 11,000 years ago, following glaciations and changes in sea level. With fewer than a thousand breeding individuals on each island, their official recognition would have urgent implications for the conservation of the insular ecosystems of the Mexican Caribbean.

Five Key Facts

Crocodiles are living fossils, masters of the evolutionary game, and guardians of a planetary history that transcends five or perhaps six mass extinctions. Not only have they survived 55 million years, these semi-aquatic reptiles have colonized fresh and salt water, firm and swampy land, continents and islands. Feared by many in the collective imagination, these predators possess the strongest bite, the most complex heart, and the most acidic stomach in the animal kingdom.

The genus Crocodylus is the most widely distributed of the crocodilians and currently comprises 14 species present in tropical and subtropical regions of almost all continents. Despite this, it was believed that only four existed in the Americas, but that is about to change.

An international team of scientists has discovered two new species of crocodiles on the islands off Quintana Roo, on the Yucatán Peninsula. Their findings challenge the long-held belief that Crocodylus acutus was a single species distributed from Baja California to Venezuela, in the neotropics.

Through genetic analysis, researchers from McGill University in Montreal, and scientists from eight universities and research centers in Mexico, in addition to the National Commission of Natural Protected Areas and the Smithsonian Tropical Research Institute in Panama, revealed that the crocodile populations on the island of Cozumel and the atoll of Banco Chinchorro present a genetic divergence so significant that it warrants classifying them as distinct species, although they have not yet been named.

The team also detected morphological differences in skulls and scales, reinforcing the genetic evidence. The research published in the scientific journal Molecular Phylogenetics and Evolution in March 2025 suggests that these endemic populations have evolved rapidly, driven by geographic isolation, extreme salinity conditions, and a specialized diet.

The crocodiles of Banco Chinchorro, for example, tolerate salinities higher than any other species of the genus Crocodylus. Furthermore, their growth is slower than that of their continental counterparts, their eggs are smaller, and their clutches are reduced, all of which points to a remarkable ecological adaptation.

The discovery not only rewrites the evolutionary history of neotropical crocodiles but also raises a conservation urgency: both populations have effectively small sizes (with fewer than 1000 breeding individuals on each island), are reproductively isolated, and face threats such as mass tourism, urbanization, and climate change. Recognizing them as new species would have key implications for their legal protection and that of their habitats, making them emblematic candidates for conservation efforts of the insular ecosystems in the Mexican Caribbean.

Cozumel and Chinchorro: Insular Ecosystems, Unique Lineages

Even a reptile would fall in love with a Caribbean island. Their turquoise waters endure, the reefs extend for kilometers, and the white sand beaches have become the setting for postcards that travel the world. Furthermore, both islands protect interior lagoons surrounded by mangroves, vital habitats for birds, fish, and crocodiles.

The Banco Chinchorro Biosphere Reserve, the largest coral atoll in Mexico, protects a dazzling biological richness and a cemetery of sunken galleons. Cozumel, the largest inhabited island in the country, holds in its reefs a tourist magnet of global scale and a Mayan cultural history that recognizes it as the sanctuary of the goddess Ixchel.

Pierre Charruau, a French herpetologist, fell in love with Chinchorro in 2003 when he first arrived as part of his master's studies. He traveled to Cozumel in 2007 to conduct genetic analyses and has since visited it frequently as well. He continued with his doctorate and is now a professor and researcher at El Colegio de la Frontera Sur. "I know these two populations very well," he states. "I have many stories, but the most surprising, looking back, is that at the beginning I saw them as different. But, since they were the populations I started studying crocodiles with, for me they became the reference for what an acutus was, and the others began to seem different to me," he recalls.

Currently, four species of crocodiles are recognized in the neotropics, which are the tropical regions of America: Crocodylus acutus, C. moreletii, C. rhombifer and C. intermedius. "The American crocodile (C. acutus) is the one with the greatest distribution across the entire continent, starting in southern Florida on the Atlantic and northern Sinaloa on the Pacific, and going down both coasts to Peru and Venezuela. They also colonized many Caribbean islands, like Cuba and even the Bahamas," explains the expert.

What the recent research reveals is that this apparent homogeneity hides deep differences. It not only challenges the canons of neotropical crocodile taxonomy but also rewrites research parameters, broadening the horizon of what could be found in insular ecosystems. "We can hypothesize that in other Caribbean islands we have the same scenario, that if one investigates like we did—the ecology, the morphology, and the genetics at the same time—new species could be found," says Charruau.

Islands as Laboratories of Adaptability

Two decades of ecological observations were needed to understand that these island populations not only survive, but thrive in extreme conditions. According to Pierre Charruau, their stability and resilience are explained by an astonishing capacity for adaptation: "At the nesting level, they have something very special. We have seen hatchlings survive category five hurricanes. They are adapted to those storms which, although they can affect them in the short term, in the long run generate new nesting areas and better reproductive conditions for them. In fact, we could say they need hurricanes to reproduce."

In Cozumel, this adaptability translates into a distinct way of nesting compared to other crocodilians. While on the continent females build mounds of vegetation that, as they decompose, generate the heat needed to incubate the eggs, on the island they dig their nests in sandbanks that storms leave exposed. There, solar energy maintains the adequate temperature for embryonic development.

This change in strategy is accompanied by other reproductive adaptations: smaller eggs, reduced clutches—fewer than 17 eggs compared to the usual 25 to 35—and offspring that reach maturity being smaller and with slower physical growth. All of these are, in the scientist's words, clear "adaptations to the limitations of the island."

In Banco Chinchorro, the challenge is different. Beyond the luminous postcard of the false atoll, its interior lagoons surrounded by red, black, white, and buttonwood mangroves hide a natural laboratory of resistance. There, the salinity reaches an average of 52.9 parts per thousand—with records of up to 65 parts per thousand—the highest levels documented for any species of Crocodylus. In other words: almost double that of the open sea.

To withstand that environment, the crocodiles have a true physiological arsenal: lingual glands that expel excess salt, a buccal epithelium—the protective tissue lining the inside of the mouth—hardened by keratin, and an osmoregulatory cloaca—the cavity that regulates the balance of water and salts. "They are adapted to the islands, and to a large extent, it's because of their diet," explains Charruau.

In Banco Chinchorro, the skulls tend to be shorter and wider, a shape associated with durophagy: a feeding behavior that involves breaking and processing hard-shelled prey (such as crabs and snails). In Cozumel, on the other hand, longer and narrower skulls predominate, a typical profile for catching fish and agile prey. On the continent, populations of the American crocodile (C. acutus) present skulls of varied shapes, from wider to more elongated, without the marked specialization of the islands.

Confirming these differences scientifically seems simple, but it is not. Everything begins in the field, with the work of Héctor González, deputy director of the Punta Sur Ecotourism Park (Foundation of Parks and Museums of Cozumel) and David Macías, park ranger of the Banco Chinchorro Biosphere Reserve (National Commission of Natural Protected Areas), finding and recovering intact skulls among mud and mangroves. Then comes the challenge of distinguishing individual traits from population or species patterns.

The pattern does not imply clear-cut boundaries; the change is gradual across the geography, without clear limits. It is like a color gradient: from blue to green, for example, with many intermediate tones where there is no exact point where one ends and the other begins. In crocodiles, that "color palette" is reflected in the shape of the skull: the snouts gradually change in proportions of length and width according to the region, with multiple intermediate forms.

To test the hypothesis, Hoi-Nam Bui, a graduate student at McGill, analyzed the shape of 43 skulls from different places using two-dimensional data. This allowed for the identification of morphological differences between populations, serving as concrete evidence in the categorization of the new species.

In summary: the shape of the skull follows the diet, and the islands push the crocodiles towards the morphological solutions that work best in their niches: catching in Cozumel; breaking in Chinchorro.

At this point, the ecological and morphological evidence indicated that the crocodile populations of Cozumel and Chinchorro could be considered cryptic species: distinct lineages that are hidden under the appearance of the same species. To the naked eye, they look so similar that traditional taxonomy overlooked the differences for decades, but upon analyzing their diet, their way of nesting, and even the proportion of their skulls in more detail, a consistent pattern of divergence emerged, though the definitive proof was still missing: looking inside their DNA.

A Supercomputer to Decode the DNA

Crocodiles are archosaurs, meaning, basically, they are living dinosaurs. Their evolutionary history dates back more than 55 million years and is particularly elusive to science. The complexity is notable: in genetic terms, crocodiles are more closely related to birds than to some other reptiles. Furthermore, these animals possess a particularity that makes their study even more difficult: the capacity for hybridization, which is the ability to reproduce with members of other species of the genus Crocodylus and produce viable offspring with intact reproductive capacities. For this and more, finding "genetically pure" populations of crocodiles is a milestone of fantastic proportions.

"The problem with crocodiles is that they all hybridize. So, in a strict sense, they don't fit the biological concept of species, because they can all mix with each other and have viable individuals. That's why they are difficult to define, in addition to the fact that crocodile taxonomy hasn't been reviewed in like a hundred years," says José Ávila Cervantes, a researcher at McGill University.

Members of the genus Crocodylus emigrated from Africa to the Americas about five million years ago, a feat made possible by their ability to swim long distances (journeys of up to a thousand kilometers out to sea have been documented). Much later, already established in the Caribbean, the populations of Cozumel and Banco Chinchorro took different paths. Demographic analysis suggests that this separation occurred about 11,000 years ago, driven by glaciations, changes in sea level, and ocean currents.

Recognized for their ecological importance, crocodiles act as "engineers" of the mangrove, as, by moving through it, they create paths that contribute to the hydrological connectivity of the ecosystems.

"It's a very complicated thing, both mathematically and genetically," warns Ávila about the demographic analysis they applied to the crocodiles of Cozumel and Banco Chinchorro. The team fed a simulation program with genetic data to test four possible scenarios about the history of these populations: without migration, with migration in one direction, in the opposite direction, or in both. The algorithm executed hundreds of thousands of repetitions to find the model that best fit the data and, from there, ran it millions of times more to refine it. This allowed them to estimate, with the greatest possible precision, how the crocodiles have moved, mixed, and separated between both islands over time.

To analyze the genetic diversity of these populations, "markers" are used, which are small points in the genome where a single "letter" or chemical base of DNA—adenine (A), thymine (T), cytosine (C), or guanine (G)—can vary. These changes, called single nucleotide polymorphisms (SNPs), allow for comparing populations and seeing whether or not they share these variants. If two populations have markers in common, it means there has been gene flow between them (they have crossed at some point). Conversely, if they have exclusive markers that do not appear in any other, they are pure lineages.

"Usually between 10 and 30 markers are used, we used 16,000," explains Avila. Although only 3% of the genome was analyzed (seeing it all would be very costly), processing that amount of data is no simple matter; it requires enormous amounts of RAM memory and computational power. "Through McGill University and the Digital Research Alliance of Canada, we had access to a supercomputer, since a normal computer, even a very expensive one, doesn't work," says the researcher. "It takes this ultra-high computational power device between 15 days and a month of continuous processing to reach the result," he concludes.

And the result was clear: the populations of Cozumel and Banco Chinchorro showed genetic divergences so deep that they correspond to genetically pure and distinct lineages from each other.

Caudal scales of a crocodile hatchling in Banco Chinchorro: unlike Cozumel, here the tail shows a more uniform pattern, with fewer irregular scales outside the main rows.

What We Don't Talk About When We Talk About Threats

"Biodiversity is disappearing faster than we can discover what we are losing," said Hans Larsson, co-author of the study and a professor at McGill University. With populations of fewer than 1000 breeding individuals and increasingly pressured habitats, nothing is certain for these species. Following the research, mass tourism, coastal urbanization, and the advance of climate change not only reduce their habitats but also multiply the pressures on ecosystems that are already limited by nature.

"Most crocodile species already face some degree of extinction threat and the accelerated development of coastal zones endangers almost all populations," warns Larsson.

Their amphibious nature and exceptional physiology—capable of even producing natural antibiotics—have allowed them to survive meteorites, glaciations, and planetary crises that wiped out much of the world's biodiversity more than once. "They are very, very resilient animals, with a huge evolutionary and adaptation history. But let's remember that many more species of crocodilians existed before: what we have today is just a fraction of what there was," explains Pierre Charruau.

Furthermore, "although they are resilient, the problem is that they now face all the threats at the same time. And, one threat plus another doesn't add up to two; together they have a much greater synergistic effect," he adds.

They are generalist carnivores, they hunt by ambush and eat almost anything that approaches them.

The discovery of these new species makes the urgency to protect them even more evident, as any disturbance could wipe out a unique genetic lineage and put an end to the living history that these animals represent.

Elevating the taxonomic status of the crocodile populations of Cozumel and Banco Chinchorro to new species would have significant consequences for their conservation. These "new" and endemic species of crocodiles can act as umbrella species, because by protecting them, the mangroves they inhabit are also safeguarded, along with the fish, crustaceans, and birds that depend on these ecosystems.

"Since they are species with a large ecological niche, if you protect them and protect where they live, you can safeguard everything that is included there," explains José Avila. And that could attract more attention and funding for the conservation of their habitats and the coexisting species, the experts indicate.

Therefore, beyond a taxonomic curiosity, this finding is a call to recognize how much we ignore about the world we inhabit and the urgent need to protect it.

"Our goal was to discover the true biological diversity of these remote ecosystems, and what we found demonstrates how little we still know," said Hans Larsson. "Now that we recognize these crocodiles as distinct species, it is crucial to protect their habitats. Limiting coastal development and implementing careful conservation strategies in Cozumel and Banco Chinchorro will be key to favoring their permanence," he added.

The discovery will be decisive, not only for strengthening their conservation but also for reimagining what the insular ecosystems of an increasingly vulnerable Caribbean still hide.