This study aims to determine species-level relationships within the genus Heteromys, as well as generic-level relationships among members of the subfamily Heteromyinae using a phylogenetic framework. Molecular sequence data were generated from two mitochondrial genes (cytochrome b and cytochrome oxidase I) and three nuclear gene segments (β-fibrinogen, engrailed protein II, and myosin heavy chain II), and analyzed under maximum parsimony, maximum likelihood, and Bayesian optimality criteria to infer relationships. Chapter 1 focuses on the phylogenetic and taxonomic implications for Heteromys from the analyses of sequence data. Phylogenies also provided a framework for delimiting species boundaries within the wide-ranging Heteromys desmarestianus complex using the Wiens and Penkrot method. Several well-supported clades within this complex were recovered, including H. goldmani, H. nubicolens, and H. oresterus, as well as five groups identified as candidate species. Heteromys oasicus was not found to be genetically diagnosable from H. anomalus, and was relegated to subspecific status. I present a revised taxonomy as follows: the monotypic subgenus Xylomys is maintained (H. nelsoni); the subgenus Heteromys is divided into three species groups – anomalus (H. anomalus [including H. oasicus], H. australis, and H. teleus), desmarestianus (H. desmarestianus, H. goldmani, H. nubicolens, H. oresterus, and the five candidate species), and gaumeri (H. gaumeri). Chapter 2 describes phylogenetic inferences made from analyses of heteromyine taxa, genera Heteromys and Liomys. Many studies have recovered Liomys as paraphyletic relative to Heteromys, and the goal of this chapter was to address this taxonomic problem. The Liomys pictus species group (L. irroratus, L. pictus, and L. spectabilis) was recovered as sister to Heteromys rather than to the L. salvini group (L. adspersus and L. salvini). I recommend a revised taxonomy for the subfamily as follows: the genus Heteromys is retained as delineated in Chapter 1; the genus Liomys is reduced in scope to include only L. irroratus, L. pictus, and L. spectabilis; the subgeneric name Schaeferia is elevated to generic rank and includes S. adspersus and S. salvini. This classification better reflects the phyletic diversity within the subfamily Heteromyinae, and requires fewer name changes; thus providing nomenclatural stability.