Abstract: We analyzed the molecular markers and morphologic traits to investigate the germplasm resources of Qingshui River common carp (Cyprinus carpio) stock. The genetic variation within populations was relatively high based on 12 microsatellite loci; the average number of alleles per locus, effective number of alleles per locus, observed heterozygosity, expected heterozygosity and polymorphism information content (PIC) were 10, 8.37, 0.54, 0.86 and 0.84, respectively. Three ancestry populations were inferred via genetic structure simulation in Qingshui River C.carpio population. A total of 105 individuals (inferred ancestry frequency >70%) were divided into three subsets according to inferred cluster, which was used for further analysis. The genetic differentiation among the subsets were at moderate level (F_ST>0.05, P<0.01). The Nei’s genetic distances among the subsets ranged from 0.473 to 0.546, and the distinct genetic structure of individuals from different subsets was detected by genetic analysis using microsatellite markers. The obvious difference of morphology was discovered among individuals, and the maximum variation coefficient was detected in body mass (38%). Significant difference existed between some pairwise subsets on morphologic traits (P<0.05), including number of hard spines of doral fin, number of scales of lateral line, number of scales above lateral line, and ratio of caudal length/body length. Forthermore, the Euclidean distance cluster results confirmed to the dendrogram based on Nei’s genetic distances. In brief, the stocks of Qinshui River C.carpio have high genetic diversity with significant genetic differentiation within the stock.