Common carp ( L.) is an important economic fish species with very rich genetic resources, and it has been used to develop many carp varieties in China. The FFRC strain (FR) and the Yuxuan Yellow River (YX) strains of common carp have higher growth performance and improved body shape, and have been certified by the National Certification Committee for Aquatic Varieties. Currently, these two carp varieties occupy a pivotal position in fresh water aquaculture because they are farmed in most provinces of China and have brought significant economic profits. Therefore, it is important to evaluate the genetic diversity of the conservation populations of these strains to maintain growth performance and make further genetic improvements. The objective of this study was to analyze the genetic structure of the breeding populations, and to evaluate the genetic distance between female and male individuals using microsatellite markers. A total of 160 and 131 alleles were detected with 23 microsatellite markers in FR (=96), respectively. For FR, the average values of number of effective alleles (), expected heterozygosity (), and polymorphism information content (PIC) were 4.559, 0.695, 0.741, and 0.702, respectively, suggesting that there is a high level of polymorphism in this strain. For YX, the mean values of , and PIC were 3.620, 0.665, 0.642, and 0.600, respectively, indicating a high level of diversity in this strain. The significantly lower P<0.01) suggested that more alleles were derived from different parents in FR with its hybrid breeding background than in YX with its systematic selection background. There was no significant difference in between FR (0.695) and YX (0.665), which indicated that YX maintains high genetic heterozygosity. The genetic distance(GD) between females and males in each population showed a normal distribution. The GD ranged from 0.8 to 1.0 and accounted for 37.39% of variability in FR, and ranged from 0.5 to 0.7 and accounted for 49.33% of variability in YX. Therefore, to construct families in breeding programs, the GD threshold is 0.8-1.0 for FR and 0.5-0.7 for YX.