Abstract: Firstly, RAPD was conducted to analyze genetic diversity of Trachidermus fasciatus in the Fuchun River population (FR), Yellow River population (YR), Luan River population (LR), and Yalu River population (YL), with 32 polymorphic 10-bp random primers selected from 294 ones. Thirty wild individuals were detected in each population.The results indicated that the genetic diversity of T. fasciatus was relatively rich. The major results were as the following:1) Altogether, 591 bands were detected and 515 of them were polymorphic, accounted for 87.14%. The range of proportion of polymorphic loci (P) was: FR(89.17%)>YR(87.99%)>YL(86.63%)>LR(83.25%). 2) The Shannon’s information index(I_T) and Nei’s genetic diversity(H_T) among populations were 0.3393 0.3566 and 0.2157 0.2279,respectively. Compare to other three populations, LR population had relative lower values. If took the populations as a whole, the total Nei’s genetic diversity(H_T) and Shannon’s information index(I_T) was 0.2336±0.1643 and 0.3710±0.2153,respectively. 3) The value of gene flow (N_m) (5.76103 19.84497) were high, indicating certain gene exchange existed among the four populations. But the AMOVA results exhibited significantly differentiation (P<0.05 or P<0.01) among the populations. 4) In the UPGMA tree constructed according to genetic distance, YL and YR populations clustered firstly, then with FR population, and finally they joined to LR population. Obviously, the YL, YR and FR populations had relatively close relationship according to their geographic distance, whereas LR population showed clear divergence to the other three populations. Secondly, out of the five special RAPD bands (S₁₂₂₅^525bp, S₁₂₂₅^605bp, S₁₂₂₅^841bp, S₁₃₄₅^695bp and S₁₃₄₅^825bp), SCAR maker SCAR01^560bp and SCAR02^443bpwere successfully transformed from S₁₂₂₅^605bp and S₁₂₂₅^841bp,respectively. After large samples examination of the two markers, we found the highest frequency (96.67% and 93.33%)in the YL population, higher frequency (83.33% and 90%) in the FR population, high frequency (56.67% and 66.67%) in the YR population, and the lowest frequency (13.33% and 20 %) in the LR population. Therefore, SCAR01^560bpand SCAR02^443bpcan be used as special molecular markers for the population identification between LR and other three populations.