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In this study, we utilized mitochondrial DNA (mtDNA) sequence data from 45 individuals of <jats:italic>C. crocodilus<\/jats:italic> throughout its range to infer its evolutionary history and population structure, as well as to evaluate genealogical support for subspecies and their geographic distributions. Our molecular phylogenetic results identified five mtDNA haplotype clades with a mean sequence divergence of 3.4%, indicating considerable evolutionary independence among phylogeographic lineages. Our results were also broadly consistent with current subspecific taxonomy, with some important additional findings. First, we found substantial genetic structuring within <jats:italic>C. c. fuscus <\/jats:italic>from southern Mesoamerica. Second, though we confirmed the existence of a widespread Amazonian clade, we also discovered a cryptic and divergent mtDNA lineage that was indistinguishable from <jats:italic>C. c. crocodilus<\/jats:italic> based on external morphology. Third, we confirm the status of <jats:italic>C. c. chiapasius <\/jats:italic>as a distinct evolutionary lineage, and provide evidence that <jats:italic>C. c. fuscus<\/jats:italic> may be moving northward and hybridizing with <jats:italic>C. c. chiapasius<\/jats:italic> in northern Mesoamerica. Finally, our results parallel previous phylogeographic studies of other organisms that have demonstrated significant genetic structure over shorter geographic distances in Mesoamerica compared with Amazonia. We support conservation efforts for all five independent lineages within <jats:italic>C. crocodilus<\/jats:italic>, and highlight the subspecies <jats:italic>C. c. chiapasius <\/jats:italic>as a unit of particular conservation concern. <jats:italic>J. Exp. 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