Several molecular markers were used in mud carp genetic diversity research. There is no choiceness varietal mud carp （Cirrhinus molitorella） in present culture. Three part of Pearl-river drainage wild mud carp （Cirrhinus molitorella） were sampled as experimentation fish，and PCR-SSCP（single strand conformation polymorphism，SSCP）was used to screen Myf5 ORF（open reading frame） DNA sequence，expecting to find SNPs relative to growth and trait. Mud carp （Cirrhinus molitorella） belongs to Cypriniformes，Cyprinidae，distributing in Pearl River，Ming River，Han River，Hainan. Taiwan and southeast of Asian. It is an important fishery production in Pearl-river drainage area. Myf5 gene （myogenic factor 5） is a member of MRFs gene family，which include Myf5，MyoG，MyoD and MRF4. The primary function of the gene family is advance myoblast multiplication and differentiation. The function of MyoD and Myf5 genes is determined to initiate the differentiation process of that muscular satellite cells to be muscle derived stem cell. And that of MyoG and MRF4 genes was thought to be involved in regulating the differentiation process of muscle derived stem cell to be myotube and muscle fibers. All of those functions were implementing by the typical trait b-HLH structure of MRF family，which form dimeric by combining with E-protein. Then Key gene is activated and pressed by the dimeric recognize upstream E-box. Many species of Myf5 gene or cDNA have been cloned. Such as Mus musculus，Bos Taurus，Sus scrofa， Ovis ammon，Gallus gallus，Danio rerio， Cyprinus carpio， Micropterus salmoide and Oncorhynchus mykiss. ） has been cloned，sequenced and analyzed by PCR-SSCP. Mud carp Genome DNA and total RNA was extracted from flesh muscle of mud carp. Myf5 gene was cloned including three exons and two introns of which the length is 453 bp，76 bp，194 bp and 1 311 bp and 90 bp（GeneBank accession：GU289508）. The cDNA sequence of Myf5 gene was obtained by RT-PCR. The length of the cDNA is 1 104 bp，and 723 bp ORF （open reading frame） was identified，which shared 93.6% homology with that of Cyprinus carpio，85.9% homology with Danio rerio. It encodes a peptide of 240 amino acids whose calculated molecular weight is 26.288 31 kD and theoretical isoelectric is 6.08. AA sequence analysis showed that the Myf5 protein have the typical trait b-HLH structure of MRF family. The population genetic information about genetic distribution，variation and heterozygosity of Myf5 gene was analyzed by using PCR-SSCP in three part of the Pearl River. The only one mutation C/T at base position 412 of the whole CDS was found among individuals in whole group. Through further analysis of the position，it could be inferred that the genotypes distribution of Myf5 in three parts of the Pearl River were not in accordance with the Hardy-Weinberg equilibrium except the north of the Pearl River subgroup，and not in accordance with the Hardy-Weinberg equilibrium in whole group. All of the three groups have high heterozygosity and moderate PIC，which indicate that the mutation is high degree in the groups and fine genetic diversity. Furthermore，there is obvious differential between observed values and expected values that indicate the evolution is discord with theory of neutral selection. In the whole of the Pearl River，A and B alleles are that not in accordance with the Hardy-Weinberg equilibrium，high degree mutation，fine genetic diversity and discord with theory of neutral selection. The number of AA type is more than that of BB type evidently，and the conclusion can be made that BB type individual has been selected. Consequently，the SNP can be used in the breeding process，avoiding the BB type as parentsFrom the molecular level，to speculate，phosphorylation switch site changed or disappeared because of the mutation，resulting in decline in individual life force. This is in the need of further experiments.