We used 1400 bp of mitochondrial DNA sequence from two gene fragments (ND4 and cyt-b) to investigate phylogenetic relationships within Atropoides, with emphasis on the subspecies of A. nummifer. Although many relationships within the genus are strongly supported, monophyly of Atropoides was never supported, although it could not be rejected with statistical confidence. In most analyses, the genus was paraphyletic with respect to Porthidium and Cerrophidion, due to the problematic placement of A. picadoi. Our results suggest that the current taxonomy may underestimate species diversity within this group. Atropoides nummifer was found to comprise three distinct phylogroups, generally coinciding with the current subspecies recognized under A. nummifer but paraphyletic with respect to A. olmec. Additionally, disjunct populations previously thought to represent A. nummifer in Oaxaca, Mexico, and Baja Verapaz, Guatemala, appear to represent A. olmec. We use the phylogeny recovered for A. nummifer and A. olmec to discuss geological and climatic events that may historically have affected gene flow within this complex.