Bats are considered reservoirs of several emerging zoonotic pathogens. Previous studies on blood parasites such as Anaplasmataceae, hemoplasmas, piroplasmids, and Hepatozoon spp. in South American bats have revealed high genetic diversity. This study investigated the molecular occurrence of these agents in 278 bats of 32 species captured in the state of Acre in the Western Brazilian Amazon. Spleen DNA samples were screened by PCR for different pathogens and tested negative for Anaplasma spp., Ehrlichia spp., Neorickettsia spp., piroplasmids, and Hepatozoon spp. However, 84 of the 208 samples (40.4%) were positive for hemoplasmas based on the 16S rRNA gene, and 15 out of the 84 (17.85%) were positive for the 23S rRNA gene. Seventeen 16S rRNA sequences, corresponding to 12 genotypes, were grouped with hemotropic Mycoplasma sp. previously detected in bats from Brazil, Peru, and Belize. Three 23S rRNA sequences represent three distinct genotypes clustered with hemotropic Mycoplasma sp., previously detected in Desmodus rotundus. This is the first molecular report of hemoplasmas in six bat species, namely Dermanura cinereus, Lophostoma silviculum, Phyllostomus elongatus, Phyllostomus hastatus, Rhinophylla fischerae, and Sturnira tildae.