Wolbachia are a group of maternally inherited bacteria that can readily spread into uninfected host populations by cytoplasmic incompatibility (CI). Theoretical studies predict that Wolbachia with higher CI levels are selected for when the maternal transmission is perfect. On the contrary, CI levels would decrease when the transmission is imperfect. Partial CIs observed in some arthropod species are explained by the imperfect maternal transmission of Wolbachia. We report here that crossing between regional strains of Callosobruchus analis show intermediate CI levels even though the maternal transmission of Wolbachia is perfect. Moreover, variations of CI levels are observed in crosses within as well as between regional strains. We will discuss probable mechanisms causing variation in intermediate CI levels in C. analis.