Phylogenetic relationships of Corallus caninus phylogeny were examined with DNA samples from five geographically disparate localities from across the range of the species (Guyana, Venezuela, Brazilian states of Pará and Rondônia, and Peru). The Peruvian sequence was the most divergent (16.2%) and the closest relative of a clade including Brazilian, Guyanan, and Venezuelan populations. Within the latter clade, the most basal lineage was from the state of Pará, followed by the state of Rondônia, which was the closest relative of populations from the Guiana Shield. Preliminary morphological data paralleled molecular results, and it is likely that a separate species of Corallus currently included in C. caninus occurs in the upper Amazon.