Tree rats of the genus Phyllomys are arboreal rodents endemic to the Brazilian Atlantic Forest. Previous phylogenetic analysis of mitochondrial DNA resulted in a basal polytomy of species in this genus, suggesting rapid speciation. Here we expanded this data matrix by adding specimens and both nuclear and mitochondrial genes. We found 2 basal clades: P. pattoni P. mantiqueirensis; and a clade split into 6 lineages: southern clade ([P. sulinus P. nigrispinus] P. dasythrix); northeastern clade ([P. brasiliensis P. lamarum] P. blainvilii); Phyllomys sp. 1; Phyllomys sp. 2; Phyllomys sp. 3; and P. lundi. The discovery of 3 potentially new species calls for a reevaluation of the taxonomy of Phyllomys species. The combination of nuclear and mitochondrial markers increased the resolution of the tree, although the basal topology is poorly supported. The patterns of geographic distribution and phylogenetic relationships are compatible with parapatric diversification within Phyllomys through ecological gradients of latitude beginning 3.69 million years ago and of altitude 4.34 million years ago.