I constructed a best estimate phylogeny based on congruence of multiple data sources. In recent years molecular data has been used both to construct phylogenies of taxonomic groups and to aid in the delimitation of new species. I generated and analyzed sequence data for forest spiny pocket mice (Genus Heteromys) for the mitochondrial gene cyt b (1143 bp) and two nuclear gene segments MYH2 (252 bp) and EN2 (189 bp). I used maximum parsimony and Bayesian analyses to infer relationships among species and to provide a framework for using a species delimitation method to investigate the possibility of multiple species within the widespread Heteromys desmarestianus. I found several well-supported lineages within the H.desmarestianus complex, including H. goldmani and H. oresterus. Incorporating karyotype and allozyme data from earlier studies, I found sufficient supporting evidence to justify maintaining H. goldmani and H. oresterus as species as well as identifying four lineages as candidate species. I present a revised taxonomic arrangement within the genus; the subgenus Heteromys should be divided into three species groups: anomalus (H. anomalus and H. australis), gaumeri (H. gaumeri), and desmarestianus (H. desmarestianus, H. goldmani, H. oresterus, and the four candidate species).