Hybridization can influence the evolutionary potential of wild species and can be especially detrimental where one species is abundant, and the other much rarer. In Belize, the Morelet’s crocodile (Crocodylus moreletii) primarily inhabits inland freshwater lagoons, lakes and rivers, whereas the less abundant American crocodile (Crocodylus acutus) is more prevalent among the offshore cayes and atolls. Both species are historically sympatric along the brackish coastline, but it is unclear if admixture between the two is affecting genetic integrity of the species. We investigated the extent of interspecific hybridization across Belize using genomic variants identified using double digest restriction-site associated DNA sequencing (ddRADseq). Five groups of genetically pure C. moreletii were identified, two of which were inland, including the protected Chiquibul National Park. Two groups of genetically pure C. acutus were identified, one on northern offshore islands, and a second along the southern coastline. Hybrids were only identified along the central-southern coastline and were in close geographic proximity to coastal purebreds. Based on these results, we suggest that the central-southern coastline represents a hybrid zone, while the inland areas and offshore islands that harbour only genetically pure populations may benefit from conservation prioritisation
