To assess genetic variations during genetic selection of Chinese softshelled turtle (Trionyx sinensis), the specimens of Chinese softshelled turtle , collected from three selected generations ( F₁,F₂ and F₃) of Yellow River population as testing group , and their base population (F₀) as well as the Taihu population as control group, were amplified by ten pairs of microsatellite primers. The result showed that: (1)A total of 240 alleles were detected in all examined loci. In all five populations the value of average allele number (N_a) were 4.60-5.30, the value of average of effective number of alleles (N_e) were 3.24-3.59; the value of average observed heterozygosity (H_o) were 0.483 3-0.530 0, the value of average expected heterozygosity (H_e) were 0.594 9-0.645 9 and the value of average polymorphism information content (C_PI) were 0.534 0-0.568 4. (2)The three selected generation’s heredity multiple parameter H_o, He and C_PI demonstrated decreased identically, along with the increases of selected generations. It indicated that the mass selection targeted on phenotypes such as growth, body color, body shape, produced a detectable effect on the genetype. (3)The phylogenetic tree showed that studied five populations were clustered into two groups, the first group consisted of the four Yellow River populations while the second group belongs to Taihu Lake population. It indicated that a significant genetic differentiation between Yellow River populations and Taihu Lake population existed and has not been changed by current three generations selection.