We obtained pharyngeal and anal swab specimens of 414 insectivorous bats. Samples of each species were pooled and then processed with a viral particle–protected nucleic acid purification method (6). The extracted RNA and DNA were amplified by sequence-independent PCR. The amplified viral nucleic acid libraries of the bat species were then sequenced with the Illumina/Solexa GAII sequencer (Illumina, San Diego, CA, USA). Those reads generated by the Illumina/Solexa GAII with length of 80 bases were directly aligned to the protein sequences in the National Center for Biotechnology Information nonredundant protein database by the blastx program in the BLAST software package, version 2.2.22 (www.ncbi.nlm.nih.gov/blast) with parameters “-e 1e-5 -F T -b 10 -v 10.” No assembly was performed before alignment. Sequence similarity–based taxonomic assignments were conducted as described (7). We found 1,075 reads of betacoronavirus in Rhinolophus pusillus bats in Shaanxi and 92 reads of betacoronavirus in Chaerephon plicata bats in Yunnan.