Abstract: To assess the genetic diversity of the wild Squaliobarbus curriculus, Inter Simple Sequence Repeat (ISSR) molecular markerwas applied from Danjiangkou Reservoir,Qinglong Lake and Suya Lake. Under predetermined optimal reaction conditions, 10 ISSR primers were selected from 77 ones. A total of 96 reproducible DNA fragments were amplified by the 10 ISSR primers from all the 90 individuals, in which 69 fragments were polymorphic, and the percentage of polymorphic loci was 71.88%. The percentages of polymorphic loci of three wild populations were 68. 13%, 64177% and63122%, respectively. The genetic distanceswere 0.1885, 0.1724 and 0.1711, respectively. The Neiπ s gene diversity was 0.1509, 0.1397 and 0.1385, respectively. Shannonπ s information indices were 012575, 012403 and 012372, respectively,which have no significant differences among the three populations (p>0.05). The genetic distances of inter-population were 011581, 011429 and 011344, respectively. The farthest genetic distance occurred between Danjiangkou Reservoir andQinglongLake populations, and the nearest between Qinglong Lake and Suya Lake. Unweighted pairgroup method witharithmetic averages (UPG MA) cluster analysis based on Neiπ s genetic distances showed that Qinglong Lake and Suya Lakepopulation assembled to one group firstly, and then did Danjiangkou Reservoir population. The results indicated that thepercentages of polymorphic loci, the genetic distances, the Neiπ s gene diversity and Shannonπ s information indices of threepopulations of Squaliobarbus curriculus were higher. The inter-population genetic distances were low, and lower than theintra population genetic distances. It showed that the three populations have high genetic diversity, but geographical geneticdifferentiation was not obvious among inter-population. The results also provided basic information for the protection andutilization of natural resource of Squaliobarbus curriculus.