The genus Rhipidomys (sigmodontine rodents in the tribe Thomasomyini) is a poorly known radiation of Neotropical mice with few studies addressing their systematics and geographic distribution. We describe 2 new species of Rhipidomys (climbing mice) from southeastern Brazil. One of these species is known only from the type locality and 2 additional sites in the southeastern part of Minas Gerais, north of the Serra da Mantiqueira mountain complex. The other species occurs to the south of this mountain range in eastern Rio de Janeiro and São Paulo states, including coastal islands. These species can be distinguished from each other and from their congeners by morphological and molecular traits, and the new species from south of the Serra da Mantiqueira has a unique chromosomal complement of 2n  =  44 and FN  =  48, 49, or 50. Phylogenetic analysis of cytochrome-b sequences also revealed an additional unnamed clade of Rhipidomys from central and eastern Brazil, which is closely related to R. cariri from northeastern Brazil. A formal description of this clade requires additional morphological analyses, including specimens from the Guianas and other central Brazilian localities. In addition, the Amazonian species R. macconnelli and R. wetzeli appear as highly divergent from all other species included in the analysis. Finally, intraspecific morphological variation in species from mesic enclaves (brejos) in northeastern Brazil indicates the need for further taxonomic revision of R. mastacalis, R. macrurus, R. cariri, and Rhipidomys sp.