Abstract: DNA methylation is an important epigenetic mechanism. It can induce changes in the biological phenotype by altering gene expression and the gene expression networks involved, thereby leading to the process of adaptive evolution. At present, epigenetic studies of polyploid genomes have been carried out in multiple aquatic animals, but epigenetic research on the polyploid genome of Crassostrea angulata has not been reported yet. In order to explore the methylation status of genomic DNA in different tissues of diploid and triploid C. angulata, the experiment used the fluorescence-labeled methylation sensitive amplified polymorphism (F-MSAP) technology to compare and analyze genomic DNA methylation in four tissues of C. angulata (mantle, gill, gonad, and adductor). The results showed that a total of 1 388 to 3 871 methylation sensitive sites were detected. The total methylation levels of the mantle, gill, gonad, and adductor muscle in diploid and triploid populations were 21.05% and 21.73%, 20.44% and 18.65%, 22.04% and 22.55%, and 21.12% and 33.56%, respectively. There were extremely significant epigenetic differences among the tissues. The full methylation levels of diploids ranged from 11.75% to 12.84%, while the hemimethylation levels ranged from 7.60% to 9.82%, and the total methylation levels ranged from 20.44% to 22.04%. The full methylation levels of triploids ranged from 11.26% to 30.28%, while the hemimethylation levels ranged from 3.28% to 10.47%, and the total methylation levels ranged from 18.65% to 33.56%. The total methylation level of triploids increased by 0.51%-12.44% compared with diploids. Full methylation was the predominant methylation mode, and the epigenetic differences between diploids and triploids were extremely significant. The research shows that the mantle, gill, gonad, and adductor muscle tissues of C. angulata have different degrees of methylation levels. Methylation changes have occurred in triploid C. angulata, and these changes may affect the way of gene expression. This study can provide reference materials for the epigenetic research of polyploid C. angulata.