The phylogeny of the neotropical palm-pitviper genus Bothriechis has been previously inferred from morphology and allozymes. These nuclear-based data sets were found to be congruent and also consilient with the geologic history of the region. We present mtDNA sequence data as an additional data set in the inference of Bothriechis phylogeny and analyze it separately and combined with previous data. The mtDNA phylogeny is incongruent with the nuclear data sets. Based on a number of factors, we hypothesize that the incongruence is due to both mtDNA introgression and lineage sorting. We argue that mtDNA represents extrinsic data and as such should be used as a consilient data set.