The Andean and Atlantic forests are separated by the open vegetation corridor, which acts as a geographic barrier. However, these forests experimented cycles of connection and isolation in the past which shaped the phylogeographic patterns of their biotas. We analyzed the evolutionary history of the Rufous-capped Antshrike (Thamnophilus ruficapillus), a species with a disjunct distribution in the Atlantic and Andean forests and therefore an appropriate model to study the effect of the open vegetation corridor and the Andes on the diversification of the Neotropical avifauna. We performed a phylogenetic/phylogeographic analysis including the five subspecies, using mitochondrial and nuclear genomic DNA, and also studied their differences in vocalizations and plumage coloration. Both the mitochondrial and nuclear DNA evidenced a marked phylogeographic structure with three differentiated lineages that diverged without gene flow in the Pleistocene (1.0-1.7 million years ago): one in the Atlantic Forest and two in the Andean forest. However, the two Andean lineages do not coincide with the two disjunct areas of distribution of the species in the Andes. Vocalizations were significantly different between most subspecies, but their pattern of differentiation was discordant with that of the nuclear and mitochondrial DNA. In fact, there is no song differentiation between the subspecies of the Atlantic Forest and that of the northwestern Bolivian Andes, even though they differ genetically and belong to different lineages. Consistently, no differences were found in plumage coloration between the subspecies of the Atlantic Forest and that of the southern Andes. Our results suggest a complex evolutionary history in this species, which differentiated both due to dispersion across the open vegetation corridor, likely during a period of connection between the Andean and Atlantic forests, and as a consequence of a geographic barrier in northern Bolivia. In both cases Pleistocene climatic oscillations appear to have influenced the species diversification.