Molecular analysis of the polymorphic region of the bovine coronavirus (BCoV)-S gene using recent Japanese field isolates and reference strains revealed that the 148 isolates collected from 1999 to 2008 from 13 prefectures, covering all regions of Japan (Hokkaido, Tohoku, Kanto, Chubu, Kinki, Chugoku, Shikoku, and Kyusyu region) and divided into 3 clusters, show distinctive divergence from the prototype enteric BCoV strains. Almost all isolates after 2005 were clustered into group 4, and there was no regional specificity in these clusters. To differentiate the genotypes without sequencing, a simple technique-reverse transcriptase-polymerase chain reaction/restriction fragment length polymorphism analysis (RT-PCR/RFLP)-was developed. The availability of a simple and easy diagnostic assay will enable larger epidemiological studies of BCoV.