Fecal samples from 56 Japanese bats representing 6 species in 2 families were examined for coccidian oocysts. Two of the 56 (<4%) were infected with coccidia; however, only 1 animal was infected with sufficient numbers of sporulated oocysts to allow the description of a new species of Eimeria. Sporulated oocysts (n = 150) of this new species are subspheroidal, 20.3 x 18.1 (16-25 x 14-21) mu m, with ellipsoidal sporocysts 10.6 x 6.6 (8-12 x 5-8) mu m; this species occurred in 1 of 4 (25%) pipistrelles, Pipistrellus javanicus (Gray, 1838) (Vespertilionidae). Oocysts of another coccidium, also an Eimeria sp., were found in 1 of 3 (33%) horseshoe bats, Rhinolophus ferrumequinum (Schreber, 1774) (Rhinolophidae), but only 2 sporulated oocysts were seen, which is not enough to describe a new species.