A molecular survey including 16,057 mosquitoes captured in Southwest Germany during the summer of 2009 showed the presence of Batai virus (BATV) in Anopheles maculipennis sensu lato. Until this survey, there was no evidence for circulation of BATV in Germany. Analysis of partial S, M, and L segments showed that the sequences from all three segments were most closely related to BATV, indicating that the virus has not undergone reassortment. Phylogenetic analysis revealed a close relationship of the isolated BATV strain from Germany with strains from Slovakia, Ukraine, and Russia.