DNA methylation was one of key epigenetic modifications in eukaryotes genomes, and has been extensively studied in the field of fishery in recent years. Here we applied MSAP (Methylation-sensitive amplified polymorphism) and analyzed the level and pattern of methylation of genomic DNA in the body wall, the respiratory tree, and the digestive tract of Apostichopus japonicus and white A. japonicus. We also compared the effects of DNA methylation in specific gene expression in different tissues of A. japonicus and white A. japonicus. In this study, a combination of 9 pairs of primers was used for the amplification of stable and clear fragments of the two populations. A total of 5932 and 5208 sites were detected in normal A. japonicus and white A. japonicus respectively, and they were mainly located at the unmethylated CCGG sites. There were 4317 and 3944 unmethylated sites in normal A. japonicus andwhite A. japonicus populations, accounting for 72.78% and 75.73% respectively. The methylation rates in the body wall, respiratory tree, and digestive tract of normal A. japonicus were about 31.07%, 23.36%, and 26.34% respectively, and those in A. japonicus were 29.88%, 23.25%, and 19.45%. These results suggested that the methylation rate in the body wall was the highest in both populations. It was inferred that the degree and pattern in DNA methylation could be different at both tissues and populations. DNA methylation may play an important role in the process of tissue differentiation and development in normal A. japonicus and white A. japonicus. Fully-methylated sites outnumbered hemi-methylated sites in the three tissues of both populations. This study provided better understanding of distinct levels and patterns of genome DNA methylation in different tissues and populations. Our findings also shed light on the relationship between the DNA methylation and the albino body wall of white A. japonicus