Abstract: Two molecular techniques, RAPD and PCR RFLP,were used to detect population genetic structure of Chinese sucker (Myxocyprinus asiaticus) from the middle reaches of Yangtze River, Yichang section (Y population),and Jinkou section (J population). Total genome DNA was isolated from fin tissue by standard phenol chloro form extraction. Four kits of primers for RAPD analysis were from Operon technologies (oph, opl, opk, opq).Nei′s genetic distance from RAPD pattern was calculated for population analysis. Of 50 RAPD primers, only 3 produced polymorphism.The genetic similarity within Yichang and Jinkou population is 0.9274?0.9313 respectively. The genetic similarity between them is about 0.9000.4μL aliquots of the PCR products of mitochondrial ND-5/6 genes were digested by 12 restriction enzymes. Estimation of mtDNA haplotype diversity followed Nei and Tajima's nucleotide diversity indices. Of 12 restriction enzymes types,11 are monomorphic except Ncil enzyme. Only two kinds of genotypes were found. The nucleotide diversity was 0.004, and the pair wise sequence divergence was about 0.235% . Meanwhile, We found differentiations between the two populations to some extent. From Ncil enzyme cleavage patterns,the restriction pattern A was predominant (about 78%) in Y population, while in J population B was the major pattern (about 88%).In RAPD patterns amplified by primer Opq02, the 1.0 kb fragments appear mainly in Y population (about 78%),while the majority of the 0.8 kb fragments appear in J population (about 88%). Because of the booming pollution, and overexploitation, and because of the longer development and the sex mature period, Chinese sucker undertook a suddenly and sharply decreasing. Bottlenecks and genetic drift came into being. On the other hand,the Gezhou Dam has been the great barrier for the gene exchange of different populations. Therefore, the genetic structure of Chinese sucker is considerably simple and there was a trend of the differentiation of gene materials among different populations.