We analyzed genetic variation in the Emerald Toucanet (Aulacorhynchus prasinus), a species complex that ranges primarily along the montane forests of southern and eastern Mexico south to Bolivia. Segments of three mitochondrial DNA genes (cytochrome b, ND2, and ND3) were sequenced for a total of 1,159 base pairs. Using maximum parsimony, maximum likelihood, and Bayesian analysis, we found a set of seven differentiated populations that correspond to clear geographic breaks throughout the highlands of the Neotropics. These genetically distinct populations also correspond with the geographic breaks found in previous analyses of morphological data. Molecular evidence suggests species treatment for four of the Central American clades and three South American clades.