After accumulating data through a nationwide survey, we characterized the recent prevalences and geographic distributions of various genotypes of infectious bronchitis virus (IBV) on layer farms in Japan. Reverse transcription PCR analysis of fecal samples revealed the presence of the IBV nucleoprotein (N) gene on approximately 30% of the farms surveyed. N-gene detection rates were higher in the Chugoku and Kyushu regions than in the remaining surveyed regions. Phylogenetic analysis of S1 gene sequences revealed that JP-I, JP-II, JP-III, and Massachusetts genotypes were particularly prevalent, with JP-I isolated throughout the country. Additionally, JP-II was the genotype detected most frequently in Chugoku, and JP-III was the most frequent in Kyushu. Unlike the previous results obtained in 1998 through 2003, the European-prevalent 4/91 genotype was no longer circulating in Japan. Moreover, the number of prefectures where multiple genotypes were detected simultaneously increased during that time.