Twelve microsatellite loci were used to investigate genetic diversity and population structure of common carp, Cyprinus carpio from Yuan River (the upper reaches of Red River in Yunnan Province, China). One hundred and ninety two samples of adult common carp were collected in 2011 from five sampling points. A total of 201 alleles were detected over all loci and the number of alleles per locus ranged from 2 to 27. There were 113 low frequencies alleles at the frequencies less than 0.05. Mean number of alleles (N_A) ranged from 12.25 to 14.67 per locus per population, effective number of alleles (N_E) ranged from 8.28 to 9.73, mean observed heterozygosity (H_O) and mean expected heterozygosity (H_E) at the 12 loci ranged from 0.7765 to 0.8037, and from 0.7761 to 0.8080, and mean polymorphism information content (PIC) ranged from 0.7534 to 0.7843. Mean number of alleles (N_A), mean effective number (N_E) of alleles, mean observed heterozygosity(H_O), mean expected heterozygosity (H_E) and mean polymorphism information content (PIC) were 16.50, 11.26, 0.7927, 0.8049, 0.7966 respectively for overall samples. The result indicated that the genetic diversity of common carp from Yuan River was abundant. An analysis on the distribution of genetic variation (AMOVA) indicated that the variation within population was very high (95.87%), while among populations was low (1.69%). The value of fixation index and gene flow were 0.0256, 9.5003 respectively for overall samples. Nei's unbiased measures of genetic identity and genetic distance among populations rang from 0.8632 to 0.9700, 0.0305 to 0.1471 respectively. This suggests that there were high genetic similarity among the 5 populations and significant genetic differentiations among the common carp individuals from Yuan River. So, the common carp from Yuan River should be managed by a population management unit. The genetic background of artificial stocking of carp larvae should not only be taken into consideration in fisheries enhancement, but also a system of evaluating the stock enhancement effectiveness should be established to prevent losing genetic biodiversity.