To resolve phylogenetic relationships among species of Marmosa we analyzed DNA sequences from one mitochondrial and three nuclear genes for every member of the nominotypical subgenus and from four species of the subgenus Micoureus. As reported in previous studies, the subgenus Marmosa was found to be paraphyletic, whereas Micoureus was recovered as a robustly supported clade. Species currently referred to the subgenus Marmosa form four strongly supported and morphologically diagnosable groups. Based on these results we recognize a total of five subgenera: Marmosa Gray, 1821 (for macrotarsus, murina, tyleriana, and waterhousei); Micoureus Lesson, 1842 (for alstoni, constantiae, demerarae, paraguayana, phaea, and regina); Stegomarmosa Pine, 1972 (for andersoni and lepida); Eomarmosa, new subgenus (for rubra); and Exulomarmosa, new subgenus (for isthmica, mexicana, robinsoni, simonsi, xerophila, and zeledoni). The best-supported hypothesis of relationships among these clades is ((Stegomarmosa (Marmosa Micoureus)) (Eomarmosa Exulomarmosa)), and our results additionally resolve many interspecific relationships within each subgenus. These clades have broadly overlapping geographic distributions, especially in western Amazonia, where the arboreal insectivorous-frugivorous niche of Marmosa is apparently partitioned among multiple sympatric congeners.