Significant efforts have been made to characterize viral diversity in bats from China. Many of these studies were prospective and focused mainly on bats that could be related to zoonotic events. However, other species of bats that are part of ecosystems identified as virus diversity hotspots have not been studied in-depth. We analyzed the virome of a group of bats collected from the Yunnan Province during 2020. The virome of revealed the presence of families of pathogenic viruses such as , , , and , among others. The viral sequences identified in were characterized by significant divergence from other known viral sequences of bat origin. Complex phylogenetic landscapes implying a tendency of co-specificity and relationships with viruses from other mammals characterize these groups. The most prevalent and abundant virus in individuals was an alphacoronavirus. The genome of this virus shows evidence of recombination and is likely the product of ancestral host-switch. The close phylogenetic and ecological relationship of some species of the genus in China may have played an important role in the emergence of this alphacoronavirus.