Thirteen microsatellite markers were used to analyze the genetic structure and genetic diversity of the breeding populations “Guanjingyang Youkuai 01” from F₁ to F₄. The results showed that the genetic diversity of the breeding population was decreasing, the average polymorphism information content (PIC) of the 13 microsatellite markers decreased from 0.638 to 0.524, the average allele number from 5.462 to 4.308, the average heterozygosity from 0.779 to 0.532, and the average Shannon’s gene diversity index from 1.356 to 1.092, respectively. The genetic identity between F₁ and its descendant generations (F₂, F₃, F₄) decreased (from 0.719 4 to 0.581 3) while the genetic distance increased. The genetic identity between the adjacent generations increased and the F_ST values decreased (0.061 9 in F₁-F₂; 0.051 1 in F₂-F₃; 0.047 5 in F₃-F₄). The allele frequency of the loci LYC0002 and LYC0054 changed regularly in the four breeding generations and they might correlate with the selected traits, which should be proved by further research. Our study suggested that the selective breeding work was efficient, some adverse genes were phased out, the hereditary basis of the population was getting pure and the genetic structure would be stable with the continuation of the breeding work.