RAPD analysis and genome in situ hybridization (GISH) were applied to research into the genetic variation of the Chlamys farreri ♀ × Patinopecten yessoensis♂hybrid scallop larvae during the four life-history stages (trochophore，D-shaped larvae，umbo-stage larvae and eye-spot larvae)．For RAPD analysis，50 random primers were used and 35 C. farreri specific bands and 28 P. yessoensis specific bands were detected in the broodstock. Different numbers of C. farreri specific bands were found in the hybrid during the four life-history stages, and the numbers were: 21 in trochophore，19 in D-shaped larvae，23 in umbo-stage larvae，and 23 in eye spot larvae. The numbers of theP. yessoensis specific bands found during these stages were 17,16,1 and 1, respectively．Meanwhile，the result of GISH analysis indicated that the hybrid scallop separately inherited one set of chromosomes (n=19) from both C. farreri and P. yessoensis broodstock during both the trochophore stage and the D-shaped larvae stage，while no P. yessoensis germ plasm was founded in the umbo-stage larvae and the eye-spot larvae．It was found that，a big transformation of the genetic composition of the hybrid happened in umbo-stage larvae when most of the paternal germ plasm was lost in the genome of the hybrid scallops．