We investigated the genetic variations in class I and class II major histocompatibility complex (MHC) genes of Schistosoma mansoni and the effects of host MHC genotypes. S. mansoni was maintained in combinations of two mouse strains with different MHC genotypes, and the MHC gene sequences of the cercariae were investigated. The detected class I MHC gene sequences were variable, with high similarity between the H-2D(b) murine host and the parasite. For other combinations, however, the parasite sequence was homologous to those of anthropoids. All class II MHC sequences detected in S. mansoni were homologous to those of anthropoids. Our results suggest that the genetic variation in the MHC sequences of S. mansoni is derived in part from the current host, indicating horizontal transfer of the sequences from mammal to parasite.