Some emerging and reemerging diseases have been associated with certain species of bats. These diseases have emerged in anthropogenic environments where the conditions for spillover of infectious agents between bats, domestic animals, and humans are present. Mexico is the country with the fourth highest bat diversity in the world, and some of these bat species live in anthropogenic environments such as a backyard production system. The objective of this study was to analyze the virome of three species of bats (Artibeus spp., Macrotus waterhousii and Pteronotus parnellii) that inhabit roosts near rural backyard farms and have large geographic distributions. Rectal swabs were taken and analyzed by the next-generation sequencing (NGS). Thus, it was possible to study the virome of these bat species which has not been previously reported. In one of them, P. parnellii, sequences of the family Coronaviridae were found. The detected viral communities of these three bat species included mostly bacteriophages while showing low numbers for known animal viruses. Viral diversities varied among the species studied and differed from previous studies. The findings of this research contribute to our knowledge of the virome of bat species which have large geographical distributions and, as in this case, inhabit anthropogenic habitats differing from intensive farms or urban settelments.