Myogenic Differentiation Antigen gene (MyoD) is a key member of the family of proteins known as myogenic regulatory factors (MRFs), which has a conserved basic helix-loop-helix (bHLH). Using RT-PCR and RACE, this paper isolated . cDNA(1090 bp) had the same 137 bp 5′-untranslated region (UTR), 50 bp 3′UTR and 903 bp open reading frame (ORF), which encoded a 350-amino-acid residues protein with the conserved bHLH domain (110-161 aa) and helix III (233-249 aa); and cDNA (1478 bp) had the same 215 bp 5′UTR, 471 bp 3′UTR and 792 bp ORF, which encoded a 263-amino-acid residues protein with the conserved bHLH domain (91-142 aa) and helix III (212-228 aa).similarity was 73%-92% between tilapia MyoD1, and the similarity was 74%-79% between tilapia MyoD2 and other fishes MyoD2. The NJ phylogenetic tree of MyoD1 and MyoD2 indicated that all vertebrates MyoD1 and MyoD2 clustered into two main branches, and fishes MyoD1 were basically consistent with the traditional classification. There was only some individual base difference between the two tilapias cDNA, and the amino acid sequence was identical to each other. The two introns of , while there was no obviously difference between the two introns of intron 2, we established one molecular marker to distinguish Oreochromis aureus♀) selected by configuration. As a result, one in fifteen The marker also provided molecular technique to select pure-blood individuals