Studies of aquatic macroinvertebrates in high-altitude rivers in the Andes are scarce, and little is known about the trophic role that these organisms play in these ecosystems. In the present work, the microhabitat preference of the aquatic macroinvertebrate community was studied and its trophic guilds was described through the analysis of stomach contents in two high Andean rivers of Peru. Significant differences (p < 0.05) were found between abundance, richness, Pielou equity index and effective number of species between the microhabitats studied in both rivers. The highest values of wealth in both rivers were found in the medium stone microhabitat, being the most abundant and diverse the members of the Diptera order. The lowest values of richness were found in the rock microhabitat. Four food items were identified: fine particulate organic matter (MOPF), microalgae (MA), animal remains (RA) and vegetable tissue (TV), of which MOPF was the predominant one in almost all the organisms analyzed, which shows that MOPF is the main food item consumed in both rivers. Spatially, it was the detritivores and herbivores that were in great proportion in almost all the microhabitats in both high Andean rivers.