Phyllomys is the most species-rich genus among spiny tree rats of the family Echimyidae and includes members widely distributed throughout the Atlantic Forest of South America. Among recognized species recovered in previous studies, 4 lineages are unnamed and their taxonomic distinctness needs further investigation. Biogeographic analyses recovered an Amazonian ancestor of the basal lineage leading to living Phyllomys, suggesting ancient connections between the 2 largest South American rainforests, and presence of rainforest corridors within the central Brazilian dry biomes. Based on exhaustive taxonomic sampling of Phyllomys, applying multigene phylogenetic methods, and morphological and karyological data, we described a new species of Phyllomys from central Brazil. Geographical records from the center of the Cerrado biome of central Brazil indicate an unexpected location for the distribution of the genus, given the contrast between the physical and biological characteristics of the Cerrado and Atlantic Forest habitats. Contrary to previous studies, the analysis of the ancestral geographic range performed here suggests a Cerrado ancestral distribution for Phyllomys during the late Miocene. This result favors the hypothesis of a past link between the Amazon and Atlantic Forest in central Brazil, through the region occupied today by the dry Cerrado, and that forest expansions and contractions may have occurred in Brazilian dry biomes over the course of the Tertiary.