Distant hybridization is the important pathway of forming hybrid vigor and polyploid individuals. By combined distant hybridization and interploid hybridization, we have obtained different ploid crucian carp. MeCP2 is a kind of DNA methylation binding protein and functions as a crucial gene expression regulator by translating epigenetic DNA methylation to proper cell response. To discover the epigenetic regulation mechanism of the reproductive ability in different ploid crucian carp, this study cloned the MeCP2 gene in different ploid crucian carp based on the transcriptome of testis. Sequence alignments indicated that there are genetic recombination and variation in genome during distant hybridization. A pair of common primers was designed to analyze the spatial and temporal expressional characteristics of MeCP2 gene during the development process of different ploid fish through semi-RT PCR and real-time PCR. The results showed that MeCP2 gene was expressed widely with the highest expression in the brain. Compared the different stages of gonadal development, the expression of MeCP2 gene decreased coupled with gonad maturation. While compared the different ploid crucian carp at the same developmental stages, MeCP2 gene was expressed significantly higher in the ovary of triploid fish than in diploid and tetraploid fish, while increased in the testis coupled with the ploid change. Taken together, the expression of MeCP2 gene is closely related to ovary maturation of different ploid fish, which lays the foundation for studying the mechanism and application of fish infertility in genetic breeding and aquaculture.