DNA methylation is related to a number of epigenetic phenomena and plays an important role in gene expression.In this study,the technique of methylationsensitive amplified polymorphism(MSAP)was used for the first time to analyze the DNA cytosine methylation of Chlamys farreri,Patinopecten yessoensis,F₁ and F₂,and we made a concrete analysis between the methylation ratio and phenotypic traits,assessed the extent and pattern of cytosine methylation between the parents and the offspring,and emphasized the discussion on the molecular basis of heterosis in terms of the DNA methylation.The results showed that,(1) DNA-methylation was negatively related to the shell length,shell height,soft body weight and adductor muscle weight,but positively related to the shell wideness and gross weight,and there was great correlativity between the DNA methylation and the adductor muscle weight(P<0.01);(2) there was a significant difference between the parents and the offspring:the methylation ratio of 5′-CCGG sites was 32.79% in P.yessoensis,24.13% in C.farreri,19.98% in F₁,and 20.18% in F₂ respectively,the methylation ratio of F₁ was less than the parents and there was no significant difference between F₁ and F₂,the alteration of the DNA methylation was the result of the cross of the parents; four classes of MSAP patterns,A,B,C and D,among hybrids and their parents were detected:pattern A,methylation levels were not changed in both parents and F₁; pattern B,demethylation,both or one of the parent was methylated,but there was no methylation in the same site in F_l; pattern C,hypermethylation,the methylation level in F₁ was higher than those in both parents; pattern D,hypomethylation,methylation ratio in F₁ was lower than those in both parents.The patterns of the F₁ DNA methylation experienced change and adjustments in order to coordinate the expression of the gene from the parents,and the DNA methylation has something to do with the expression of heterosis.