Abstract: The present study aimed to examine the genetic diversity and genetic structure of the successive selective breeding populations of Cyprinus carpio rubrofuscus from F₁ to F₄ generations by using 16 microsatellite markers. The results showed that 99 alleles were detected among 16 polymorphic microsatellite loci. The number of alleles detected on each locus varied from 3 to 10, and the average number of alleles was 6.1875. From F₁ to F₄ generations, the average number of alleles for 16 microsatellite markers decreased from 5.6875 to 4.6755, the average of heterozygosity ranged from 0.7943 to 0.7135, and the average of polymorphism information content (PIC) reduced from 0.6577 to 0.5834, respectively. The genetic distance between F₁ and its descendant generations (F₂-F₄) increased from 0.1486 to 0.2181, while the genetic identity decreased from 0.8619 to 0.8041. The values of genetic differentiation index (F_st) between the adjacent generations decreased (0.062 between F₁-F₂; 0.058 between F₂-F₃; and 0.051 between F₃-F₄), whereas the values of genetic identity increased. Pairwise values of F_st ranged from 0.05 to 0.15, reflecting that the selective breeding populations contained moderate genetic differentiation among four generations and the genetic structure has been varied from one generation to the next one through selective breeding. This study suggested that the selective breeding was an efficient approach, and there was a decrease in genetic heterozygosity and genetic diversity, while high genetic diversity and genetic potential were maintained in the selective breeding populations, indicating that there is a great potential for future selections of Cyprinus carpio rubrofuscus through selective breeding. Our study provides precious information for genetically breeding in Cyprinus carpio rubrofuscus as well.