We report the genetic analysis of a pigeon circovirus (PiCV/Japan/2/2010) detected in a racing pigeon with diarrheal symptoms in western Japan. Sequencing revealed a genome size of 2,041 bp that contained 3 open reading frames (ORFs), designated V1, C1, and C2, a structure consistent with to those of other pigeon circoviruses. Phylogenetic analyses of the ORF C1 revealed that PiCV/Japan/2/2010 diverges from other Asian pigeon circoviruses, suggesting genetic diversity of pigeon circoviruses in Asia.