Background Recent phylogenies of deer mice, genus Peromyscus, have relied heavily on mitochondrial markers. These markers provided resolution at and below the level of species groups, but relationships among species groups and Peromyscus affiliated genera have received little support. Here, we present the mitochondrial genomes of 14 rodents and infer the phylogeny of Peromyscus and related taxa. Results Our analyses support results from previous molecular phylogenies, but also yield support for several previously unsupported nodes throughout the Peromyscus tree. Our results also confirm several instances of paraphyly within the clade and suggest additional taxonomic work will be required to clarify some relationships. Conclusions Our findings greatly enhance our understanding of the evolution of Peromyscus providing support for previously unsupported relationships. However, the results also highlight the need to address paraphyly that may exist in this clade.