Genetic variation in the common bush-tanager Chlorospingus ophthalmicus complex in Mesoamerica was studied. An 800-bp mitochondrial DNA fragment, including a portion of COII, full tRNA-Lys, ATP8, and partial ATP6, was sequenced and analyzed for 96 individuals of the species and related taxa, resulting in a detailed framework of genetic differentiation in the northern half of the distribution of the complex. Phylogenetic analyses based on maximum parsimony, maximum likelihood, and Bayesian optimality criteria found deep divergence between South American and Mesoamerican isolates, and seven differentiated populations corresponding to clear geographic breaks across the highlands of Mesoamerica. These distinct populations coincide with geographic structure found in previous analyses of morphological and molecular data for Chlorospingus ophthalmicus, as well as in previous phylogeographic studies of other taxa in the region. Species status for these populations is discussed under the evolutionary and biological species concepts.