Twelve microsatellite markers from silver crucian carp were used to investigate the genetic structuring of the diploid and triploid crucian carp from six natural populations in Heilongjiang River System. In the six populations, the number of average allele (A) is from 5.8 to 6.8, the number of effective allele (Ne) is from 2.8 to 4.6, the expected heterozygosity value (He) is from 0.5592 to 0.6962 and the average PIC value is from 0.5962 to 0.648, which indicated that the genetic diversity of the populations investigated is rich. According to genetic deviation index (d), deviation from Hardy-Weinberg equilibrium was found in these populations and all of them showed heterozygosity excess. Kruskal-Wallis test indicated that there was no significant variance in different ploid level and populations. No extra alleles that present with the increase of ploid level were found. The coefficient of gene differentiation between populations(GST)was 0.0398 which indicated low values of genetic differentiation between these populations. Genetic distance was calculated and cluster analysis was also carried out. The results showed that distance between polyploid and diploid in same water was the nearest. Among populations, Songhua River and Ussuri River were the nearest, Xinhuangpao Lake and Moon Bay Lake were nearer, and Shuangfeng reservoir has the largest genetic distance with others.