Abstract: Brass gudgeon(Coreius heterodon) is an endemic species in China,and mainly distributes in the upper and middle sections of the Yangtze River.The fish population has been greatly decreased these years due to various factors,such as destruction of spawning condition,water pollution,over exploitation and so on.In order to protect the fish population,it is necessary to study genetic diversity of the fish population.The fish specimens were collected from 9 sampling locations in the upper and middle sections of the Yangtze River,i.e.,Hechuan(HC),Mudong(MD),Fuling(FL),Wanzhou(WZ),Wushan(WS),Sandouping(SDP),Yichang(YC),Yueyang(YY) and Jinkou(JK).The specimen number was in Tab.1.The mitochondrial D-loop region(control region) of the fish was amplified by polymerase chain reaction(PCR) technology and sequenced with ABI 3730 sequencer.100 sequences were analyzed using some softwares,viz.,Clustal X 1.83,MEGA 3.1,DnaSP 4.50.3 and Arlequin v3.01.The results were as follows:Every specimen sequence was 946 bp for genetic diversity analysis of the fish.Both 47 mutations of nucleotide acids including 8 inserting or deleting ones and 41 haplotypes were found in the 100 sequences.About 34% of the 41 haplotypes presented at least in two or more geographic groups and every one of 27 haplotypes just appeared in single one of the 9 groups.The UPGMA tree and the Parsimony network of 41 haplotypes showed that the clustering of haplotypes did not correspond to every geographic group of the fish.Genetic structure analysis showed a low level genetic diversity of C.heterodon(Hd=0.9257?.0162,Pi=0.004178?.002337).The AMOVA analysis indicated that 99.66% of the total variation in D-loop region sequence came from nucleotide acid mutations of the fish individuals in the 9 geographic populations,and just 0.34% from variation between the 9 geographic populations,which showed little genetic differentiation between the 9 geographic groups.Meanwhile,average Kimura 2-parameter distances(Tab.6),the FST value(Tab.4) and Nm value(20.84) also revealed little genetic differentiation between the 9 geographic groups.All the data mentioned above indicated that the 9 geographic groups belonged to single nature population.