Among several factors proposed as drivers of species diversification in the American tropics, the riverine barriers hypothesis plays a central role in Amazonian biogeography, being observed in many species. Although the hypothesis has great evolutionary importance, some species deviate from the expected biogeographic pattern. Their evolutionary histories are better explained when considering climatic oscillations or joint action of climatic fluctuations and river dynamics. Here, we used reduced representation genome sequencing and species distribution models to better understand the implications of landscape dynamics and climate shifts on species diversification in the Neotropics. The blue-crowned Manakin (Lepidothrix coronata) has one of the widest distributions amongst Manakin, with remarkable phenotypic variation across its distribution, thus an excellent model for this sort of study. We found evidence for the existence of four, geographically structured, evolutionarily independent lineages that diverged close to the Pliocene-Pleistocene boundary. Despite distribution models indicating habitat suitability crossing the rivers, we found no evidence of gene flow between the lineages, suggesting that the diversification process was mainly triggered by vicariant events, such as the establishment of the Amazonian rivers and the rise of the northern Andes.