Abstract: Single nucleotide polymorphisms (SNPs) of MyoD gene were analyzed in 100 Japanese flounder with PCR-SSCP Association between the polymorphisms and growth traits were analyzed. The results showed that the polymorphism sites were identified in exon 1(MyoD2) and intron 1(MyoD4). Three genotypes were found at the MyoD2 locus, denoted AA, AB and BB, and polymorphism site was G863A, being synonymous mutation. DD, FF, CD, CE, DE and DF genotypes were found at the MyoD4 locus. The association between different genotypes and Japanese flounder growth traits were analyzed by leastsquare analysis. The results indicated that there was no significant effect in the SNPs of exon 1 on growth traits (P0.05), the SNPs in intron 1 were significantly associated with the body weight, body length and body height (P0.05). These SNPs might be useful for a further research on MyoD genes relation to production performance in Japanese flounder.