Amazonia is a great natural laboratory, allowing the study of complex evolutionary mechanisms that promote diversification associated with dynamic geomorphological, climatic, and ecological processes, which often generate fuzzy species boundaries. We investigated the evolutionary history of two sister species of nurse frogs distributed in northwestern Amazonia, Allobates insperatus and A. juami, which have been considered as different entities based on molecular evidence, despite the absence of substantial phenotypic differences. We obtained morphological, osteological, and acoustic data, and DNA sequences of one mitochondrial and six nuclear gene fragments across the species distribution. The mitochondrial tree and species delimitation methods suggest the existence of at least four main evolutionary lineages; however, the signal of the nuclear markers is discordant among some groups, showing the admixture of those lineages that may reflect introgression and/or incomplete lineage sorting. Considering all sources of evidence, we confirm A. insperatus and A. juami as valid species and redescribe the former. In addition, we recognize and describe a new species supported by all data and analyses. Our findings suggest that speciation of Allobates, and perhaps of other sympatric anurans, in western Amazonia may have been influenced by the Pebas megawetland, with subsequent dispersion through the Andean foothills before the formation of the main Amazonian rivers, followed by colonization of the emerging northwestern Amazonian lowlands and secondary contact of newly diverged sister lineages.