Comments: No subspecies are recognized, although geographic variation exists among populations in Florida, Jamaica, and the Pacific coast. Populations in Florida, Jamaica, and the Dominican Republic differ from each other in their gene frequencies (Menzies and Kushlan 1991). Densmore and White (1991) used molecular data to assess phylogenetic relationships within the Crocodylia, including all species in the genus Crocodylus; the closest relative of C. acutus was C. intermedius by one analysis using rDNA, C. moreletii by another analysis that used both rDNA and mtDNA; overall, New World species of Crocodylus appeared to be more closely related to each other than to species in other parts of the world. See Ernst et al. (1999) for further taxonomic discussion.

Milián-García et al. (2011) examined microsatellite loci plus DNA sequence data from nuclear (RAG-1) and mitochondrial (cytochrome b and cytochrome oxidase I) genes of Crocodylus acutus and C. rhombifer from Cuba. They found that C. acutus from Cuba is more closely related to C. rhombifer than to C. acutus from Central America. Thus current taxonomy does not appear to be an accurate reflection of evolutionary relationships. The researchers also found evidence of hybridization between the two species in Cuba. Further study is needed before taxonomic issues can be resolved. (Milián-García et al. 2011).