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Aim Little is known about factors affecting the elevational and longitudinal zonation of tropical Andean stream communities. We investigated epilithon, macroinvertebrate and fish assemblages along a 4100-m elevational-longitudinal gradient in an Andean headwater of the Amazon Basin. We interpret our results within the context of environmental factors, emphasizing temperature, as well as ecological theory relating shifts in metazoan functional feeding groups to shifts in basal resources along the fluvial continuum. Location Arazá-Inambari-Madre de Dios watershed, south-eastern Peru. Methods We sampled water physicochemistry, epilithon and macroinvertebrate diversity and abundance, and fish diversity at 18 main-stem and 14 tributary sites from high puna grasslands (4300 m a.s.l.) to Amazon Basin lowlands (200 m a.s.l.). Results Water physicochemical parameters and the taxonomic and ecological structure of invertebrate and fish assemblages displayed mostly nonlinear responses to elevation: water temperature and percentage of macroinvertebrate taxa identified as leaf shredders had U-shaped responses; dissolved oxygen and percentage of macroinvertebrate taxa identified as grazers had hump-shaped responses. Epilithon richness increased slightly with elevation whereas macroinvertebrate and fish richness decreased. Main conclusions Elevational gradients in physicochemical parameters are insufficient to explain abrupt and nonlinear shifts in community taxonomic and functional structure. Rather, trophic interactions, including predation and longitudinal turnover in basal food resources, seem to exert a stronger influence on the distributions of Andean aquatic organisms. A steep elevational decline in relative taxonomic diversity of leaf-shredding (versus algae-grazing) insects supports the hypothesis that temperature affects the functional composition of insect assemblages via its influence on microbial decomposition rates. This relationship, and the distributions of several insect and fish species across narrow elevational bands, suggests that Andean stream communities may be sensitive to global warming. Placer mining and road building impacts have already altered stream community structure, including the absence of many benthic species from low-elevation habitats. [ABSTRACT FROM AUTHOR]