The evolutionary history of Neotropical crocodiles has remained elusive. They inhabit a broad geographic range with populations spanning from coastal, inland, and insular locations. Using a selection of natural insular, coastal, and one inland populations of C. acutus, coastal C. moreletii, and the single surviving population of C. rhombifer, we discovered a remarkable genetic diversity for the group. Moreover, geometric morphometric results of skull shapes shows that these crocodylus species span a morphological cline. We recovered a high genetic differentiation between C. moreletii, C. rhombifer, and five clusters of C. acutus. The genetic and geographic differences among the C. acutus clusters were used to suggest these may be a species complex.Several ecological, morphological, and genetic traits are identified in the well-studied population from Banco Chinchorro and Cozumel islands off the Mexican Yucatan Peninsula to support discrete species designations for these populations. This work suggests the presence of rapid, recent evolution of several cryptic Crocodylus species throughout the Neotropics.