Abstract:DNA methylation plays an important role in regulating gene expression, cell aging and trait differentiation. In order to investigate the differences of DNA methylation level and pattern in different genders and tissues of Sepia esculenta Hoyle, we applied Fluorescence-labeled Methylation Sensitive Amplified Polymorphism (F-MSAP) technology and analyzed the level and pattern of methylation of genomic DNA in the muscle, the heart, the pancreas and the gonad of female and male S. esculenta. The total methylation rate of S. esculenta in the growing stage was 23.97%~39.70%, which was at a high level in aquatic invertebrates. Among the female and male's four tissues, the total methylation level in muscle was the highest, which may be related to the phenomenon of allometric growth and the preferential development of the muscle during the growing state. Moreover, both the methylation levels and patterns of S. esculenta were different in gender, the total methylation level of DNA in the muscle tissue of the female S. esculenta was significantly lower than that of the male, but that in the heart and pancreas tissue was significantly higher than that in the male. In addition, we also found that the fully methylation level in the muscle of female S. esculenta was the largest contributor to the total methylation level and was consistent with the level of total methylation in the other tissues of female S. esculenta and in the four tissues of male S. esculenta. The results showed that the level and pattern of DNA methylation of S. esculenta had gender and tissue differences. This study can provide basic data for epigenetic regulation of the life processes such as the growth, differentiation, and death of S. esculenta.