Two viruses were isolated from bovine blood in the southernmost part of Japan in 1994 and 2001, respectively. Genetic analyses showed that the viruses were Batai virus of the genus Orthobunyavirus of the family Bunyaviridae. The sequencing of three genomic RNA segments of the Japanese and Malaysian Batai virus strains revealed that the M RNA segment of Batai virus had high sequence identity with that of Ngari virus. Our results indicate that Ngari virus is a genetic reassortant with S and L RNA segments from Bunyamwera virus and an M RNA segment from Batai virus.