We induced the gynogenetic offspring of the breeding grass carp (YZ) using UV-inactivated grass carp sperm and cold shock method to inhibit extrusion of the second polar body. Twelve pairs of microsatellite primers were used for amplification and genetic analysis of the YZ population and control population (YS). A total of 194 alleles were detected in the YZ and YS populations, of which 75.8 were effective alleles. The average number of alleles in the YZ, YS and CH populations was 13.0, 12.6, and 4.7, respectively; the average number of effective alleles was 7.7, 6.6, and 2.3, respectively; the average expected heterozygosities were 0.87, 0.82, and 0.56, respectively; and the average polymorphism information content was 0.84, 0.79, and 0.49, respectively. Homozygosity was analyzed for the microsatellite loci:the homozygosity of individuals in the YZ population was 0.00-0.33, the homozygosity of individuals in the YS population was 0.00-0.42, and the homozygosity of individuals in the CH population was 0.42-0.92. The results showed that the genetic diversity of the CH population was significantly lower than that of the YZ population and the YS population, and the homozygosity of the CH population at each locus was higher than that of the common grass carp groups. This suggests that artificially induced meiotic gynogenesis can accelerate the homozygosity of most grass carp gene loci and is an effective means of rapidly establishing a high purity strain. At the same time, this study screened and used microsatellite loci combinations to establish a simple and efficient identification technique for the genetic relationship among different families and their female parent, laying a foundation for the marker-assisted breeding of gynogestidium.