Abstract: To assess the genetic diversity and population structure of Monopterus albus, 178 individuals of 6 populations (DT, WW, FC, GC, HN, WJ) from Anhui reaches in the Yangtze River were investigated based on 556-558 bp nucleotide sequences of mtDNA partial control region. The sequences analysis results showed that 41 variable sites (mutation rates of 7.35%), 56 haplotypes were detected. The haplotype diversity (Hd) and nucleotide diversity (Pi) were 0.694-0.954 and 0.00237-0.01382, respectively. Analysis of molecular variance (AMOVA) revealed that genetic variation among the populations was 61.72%. These results indicated that there were significant genetic differentiations among populations. NJ-tree based on haplotypes or genetic distances among populations showed that DT and FC populations were clustered as one, and other 4 population was as another independent cluster.