Accurate estimates of species diversity are essential for all biodiversity research. Delimiting species and understanding the underlying processes of speciation are also central components of systematic biology that frame our comprehension of the evolutionary mechanisms generating biodiversity. The South American tree squirrels (genus Guerlinguetus) are keystone mammals, widely distributed, that are critical in tree-seed predation and dispersal in one of the most fragile and threated ecosystems of the world, the tropical rainforests of South America. We obtained genomic data (ultraconserved elements and single nucleotide polymorphisms) to explore alternative hypotheses on species limits of this genus and to clarify recent and rapid speciation on continental-scale and dynamically evolving landscapes. Using a multilayered genomic approach that integrates fine-scale population genetic analyses with quantitative molecular species delimitation methods, we observed that (i) the most likely number of species within Guerlinguetus is six, contrasting with both classic morphological revision and mitochondrial species delimitation; (ii) incongruencies in species relationships still persist, which might be a response to population migration and gene flow taking place in the lowlands of eastern Amazonia and/or to the extremely rapid successive speciation events; and (iii) effective migration surfaces detected important geographic barriers associated with the major Amazonian riverine systems and the mountain ranges of the Guiana Shield. In conclusion, we uncovered unexpected and higher species diversity on Guerlinguetus and corroborate recent findings suggesting that much of the extant species-level diversity in Amazonia is young, dating back to the Quaternary. We also reinforce long-established hypotheses on the role of rivers and climate-driven forest dynamics in triggering Amazonian speciation.