SRAP (Sequence-related amplified polymorphism) markers and mitochondrial DNA control region sequencing were used to investigate genetic structure of four loach (Misgurnus anguillicaudatus) populations from two sympatric distribution areas of natural diploid and tetraploid loach-Dongting Lake (DT) and Wuhan city (WH) in China.The results from SRAP showed that a total of 534 loci were detected in four loach populations by 18 pairs of polymorphic primer combinations,and the numbers of amplified loci per primer pair ranged from 23 to 40.The averages of Nei’s gene diversity (h) and Shannon’s information index (I) of each population were from 0.205 to 0.218 and from 0.324 to 0.341,respectively,and there were no significant difference among h-values or I-values of four populations.UPGMA dendrogram tree,which was constructed based on the Nei’s unbiased genetic distances,showed that DT diploid and DT tetraploid populations were firstly clustered into one branch and their relationships were the nearest,then WH tetraploid population was clustered to the branch.And the other branch contained only WH diploid population.Partial sequences of mitochondrial control region (932-935 bp) of 40 individuals representing four loach populations were sequenced.A total of 47 nucleotides were variable,resulting in a total of 29 haplotypes.Nucleotide diversities (π) of DT tetraploid and DT diploid within populations were 0.898% and 0.872%,respectively,and they were significantly larger than those of WH tetraploid (π=0.465%) and WH diploid (π=0.675%).Within the sympatric diploid and tetraploid loach populations,genetic diversity of DT tetraploid was larger than that of DT diploid,and the genetic diversity of WH diploid was significantly larger than that of WH tetraploid.Analysis of molecular variance (AMOVA) indicated that the genetic variation mainly occurred within populations (63.55%),and 37.32% of variation occurred among populations.Significant population subdivision was supported by both pairwise FST values and Kimura 2-parameter genetic distances between populations,except for no apparent subdivision between DT tetraploid and DT diploid.Phylogenetic tree through Bayesian inference from the control region sequence haplotypes was similar to the genetic relationship among four loach populations revealed by SRAP analysis.