. We used MSAP (Methylation-Sensitive Amplification Polymorphism) to analyze methylation patterns of genomic DNA in the muscle, gill, and blood of wild and cultivated “Huanghai No.1”, a strain selected for faster growth rates and improved disease resistance. DNA methylation is closely linked to biological events, including chromatin inactivation, transgene silencing, genomic imprinting, and control of parasitic DNA elements. Because of its efficiency and competence, the MSAP technique has been increasingly used in genomic DNA or individual functional genes studies to analyze DNA methylation levels. We used 30 pairs of selective-amplification primers. Using polyacrylamide gel electrophoresis, we estimated the methylation ratios in the muscle, gill, and blood of wild stock were 23.1%, 22.3%, and 19.7%, respectively, and 21.4%, 19.6%, and 18.9%, respectively, in cultured shrimps. These levels are much lower than in some plants and animals, perhapsbecause of differences in the amount of genomic DNA. The methylation levels at the CCGG site differed among different tissues of the same stock and between the same tissue among different stocks. The level of methylation in genomic DNA was always higher in the organs than in the blood. We observed variation in the DNA polymorphic methylation between wild and “Huanghai No.1” stocks in the blood and gill, but not in the muscle. Furthermore, polymorphic methylation was associated with demethylation and methylation of CCGG loci. Additional research is needed to understand the biological meaning of variation in methylation among CCGG loci. Our approach provides a basis for further studies on the mechanism of methylation-mediated DNA methyltransferases in .