Myostatin (MSTN) is a member of the transforming growth factor-β superfamily that negatively regulates skeletal muscle development and growth. In the present study, partial genomic fragments of MSTN were screened for single nucleotide polymorphisms (SNPs) in a hybrid of Culter alburnus (♀) x Ancherythroculter nigro-cauda (♂) individuals from a commercial hatchery population, and two non-synonymous SNPs (c.6T>C and c.162G>A) and two synonymous SNPs (c.152G>A and c.155G>A) in exon 2 were identified. The two non-synonymous SNPs caused an amino acid change, from Ser to Pro and from Val to Ile, respectively. Genotyping by the direct sequencing of polymerase chain reaction products for these four SNPs was conducted in 190 individuals from the commercial hatchery population. Association analysis showed that one non-synonymous SNP (c.6T>C) in exon 2 was significantly associated with total length, body length, body height, head length, and body weight. Haplotype analyses revealed that the haplotype combination H1H3 exhibited the best growth performance. Our results demonstrate that some of the SNPs in MSTN may have positive effects on growth, and suggest that MSTN could be a candidate gene for marker-assisted selection in C. alburnus and A. nigrocauda.