The DNA methylaiton extent and patterns of CCGG sites in the genome of the Pacific oyster () was investigated among six different tissues using the fluorescence-labeled methylation-sensitive amplified polymorphism (F-MSAP) method. The incidence of DNA methylaiton in the six tissues (gill, adductor, mantle, labial palp, gonad and digestive glands) was 31.77%, 36.41%, 32.00%, 36.47%, 32.77% and 37.92%, respectively. DNA methylation patterns can be divided into two types: the fully methylated and . The fully methylated loci showed similar trend with the total methylation level: digestive glands, labial palp and adductor showed much higher methylation level than the other three tissues and the difference between the six tissues was significant (<0.05). The rate of hemimethylated loci is less than the fully methylated loci and not significantly different between the tissues. Both (bands methylated or unmethylated in only one of the six tissues) and tissue nonspecific differentially methylated regions (bands methylated or unmethylated in more than one of the six tissues) were found in Pacific oyster, but these two kinds of bands only occurred in one or few individuals. No tissue specific/nonspecific differentially methylated regions were found in all individuals analyzed and this might correlate with the high polymorphism in the Pacific oyster. Fluorescence-labeled amplified fragment length polymorphism (F-AFLP) showed the percentage of polymorphism loci was 87.5%, and the expected heterozygosity ranged from 0.267 0 to 0.347 5. Results from F-MSAP and F-AFLP indicated that genetic variation might contribute to the DNA methylation patterns.