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Bumble bees of the genus Bombus spp. play a key role as effective pollinators in the biodiversity rich Central Andean region; however, parasites and pathogens may negatively influence their abundance and population numbers. In this study, we aimed at verifying the occurrence of these natural enemies in the Andes regions of Bolivia and Peru. Workers and males of Bombus funebris, Bombus opifex and Bombus pauloensis were collected in three localities from highlands at ~1,700 m.a.s.l. Analyses by both optical and molecular techniques revealed the presence of the Apis mellifera filamentous virus (AmFV), the microsporidium Vairimorpha ceranae, the flagellates Crithidia bombi and Lotmaria passim, and five species of mites in the genera Parasitellus Willmann, Pneumolaelaps Berlese, Proctolaelaps Berlese, Tyrophagus Oudemans, and Kuzinia Zachvatkin. Given the potential entry of the allochthonous bumble bee Bombus terrestris to the region, this information is essential to evaluate autochtonous biodiversity conservation strategies. [ABSTRACT FROM AUTHOR]