We describe a new species of woolly mouse opossum from northwestern Amazonia, Marmosa jansae, based on museum specimens previously misidentified either as M. germanaThomas, 1904, or as M. reginaThomas, 1898. Instead of being closely related to either of those species, M. jansae appears to be the sister taxon of M. perplexaAnthony, 1922, a trans-Andean species previously synonymized with M. phaea Thomas, 1899. We redescribe M. perplexa, which inhabits critically endangered evergreen and semideciduous forests in southwestern Ecuador and northwestern Peru. We also redescribe M. germana, an Amazonian species that has long been synonymized with M. regina, but which molecular analyses now suggest is the sister taxon of a trans-Andean species complex that includes M. alstoni (Allen, 1900). These results substantially clarify the long-confused taxonomy of woolly mouse opossums (subgenus Micoureus), provide new examples of sister-group relationships between upper-Amazonian and trans-Andean taxa, and raise interesting questions about congeneric diversity in northwestern Amazonia, where as many as six species of Marmosa might occur sympatrically.