Bats have great potential as reservoirs for emerging viruses such as severe acute respiratory syndrome- coronavirus. In this study, bat coronaviruses (Bt. CoVs) were detected by RT-PCR from intestinal and fecal specimens of Miniopterus fuliginosus breeding colonies in Wakayama Prefecture caves, where we previously identified bat betaherpesvirus 2. Two primer sets were used for the detection of Bt. CoV: one was for the RNA-dependent RNA polymerase (Rd. Rp) region and the other was for the spike (S) protein region. Eleven and 73% of intestinal and fecal specimens, respectively, were positive for Rd. Rp region, and 2 and 40% of those were positive for S protein region. Sequencing and phylogenetic analysis showed that the detected Bt. CoV belonged to the group 1 (alpha) coronaviruses. These data suggest that Bt. CoV is endemic in M. fuliginosus in Japan. ยฉ Springer Science+Business Media, LLC 2011.