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The genus Marmosa contains 15 currently recognized species, of which nine are referred to the subgenus Marmosa, and six to the subgenus Micoureus. Recent revisionary research based on morphological data, however, suggests that the subgenus Marmosa is more diverse than the currently accepted taxonomy indicates. Herein we report phylogenetic analyses of sequence data from the mitochondrial cytochrome-b gene representing 12 of the 14 morphologically defined taxa recently treated as valid species of Marmosa (Marmosa) in the aforementioned revisionary work. These data provide a basis for testing the monophyly of morphologically defined taxa in the subgenus Marmosa, and they afford the first opportunity to assess phylogenetic relationships among the majority of species currently referred to the genus. Ten of 11 species of Marmosa (Marmosa) represented by multiple sequences in our analyses were recovered as monophyletic. In contrast, our samples of M. mexicana were recovered as two deeply divergent haplogroups that were not consistently associated as sister taxa. Among other results, our analyses support the recognition of M. isthmica and M. simonsi as species distinct from M. robinsoni, and the recognition of M. macrotarsus and M. waterhousei as species distinct from M. murina. The validity of three other species long recognized as distinct (M. rubra, M. tyleriana, and M. xerophila) is also clearly supported by our results. Although cytochrome-b sequence data are not consistently informative about interspecific relationships in this study, we found strong support for several clades, including (1) the subgenus Micoureus; (2) a group comprised of Marmosa macrotarsus, M. murina, M. tyleriana, and M. waterhousei; (3) a group comprised of M. robinsoni and M. xerophila; and (4) a group comprising all of the species in the subgenus Marmosa that occur north and west of the Andes (M. isthmica, M. mexicana, M. robinsoni, M. simonsi, M. xerophila, and M. zeledoni). Our discovery of the latter clade suggests that the Andes may have played a major role in the early diversification of this speciose radiation of small Neotropical marsupials.