Based on recent discoveries, Bujurquina appears to be the most widely distributed and species-rich cichlid genus in the western Amazon of South America. In this study, using a large representative sample of Bujurquina covering its whole distribution area, we use morphological and molecular data to test the hypothesis that each major western Amazon basin includes multiple endemic Bujurquina species arranged along an elevational river gradient and that these species are upland- and lowland-adapted in their ecomorphology. The hypothesis derives from two lines of evidence, i.e. observations of distribution patterns in Bujurquina and paleogeographic reorganisation of western Amazon drainage patterns. Body shape morphometrics and a biogeographic reconstruction of molecular phylogeny supported our hypothesis, confirming that upland and lowland Bujurquina show consistent differences in body shape and proportions that can be explained as repeated adaptations to local aquatic conditions within each main river basin. Ecomorphological divergence in relation to lentic and lotic waters (lowland and upland habitats) was repeated in all five basins studied, i.e. the Madre de Dios, upper Ucayali, central western Amazon-Huallaga, Marañón and Napo-Putumayo basins.