Using a PCR-based method, we detected Wolbachia in the Asian rice gall midge. Furthermore, results showed that all females across all biotypes are infected with Wolbachia. However, all male flies are not infected and show different infection frequency in different biotypes. We have also identified three mitotypes, in the rice gall midge, based on DraI restriction pattern of a portion of the 12S rRNA gene that was PCR amplified using primers specific to this gene. All the females and infected male flies had type 1 mtDNA while uninfected males showed only type 2 or 3 mtDNA. Inheritance patterns of mtDNA revealed the existence of a correlation between mtDNA type and Wolbachia infection in the Asian rice gall midge. Evidence for paternal inheritance of mtDNA in Wolbachia-free gall midge is also presented.