This study examines the effects of sample size on various genetic structure parameters. The population genetic structure of cultured mirror carp (Cyprinus carpio) was estimated using microsatellite markers. 8 different sample sizes and 5 marker numbers were set up to analyze most genetic parameters including population alleles distribution, allele numbers(A), effect allele numbers(Ae), observed heterozygosity(Ho), expected heterozygosity(He) and polymorphism information content(PIC). As a results, population allele numbers rise dramatically along with sample sizes from 10 to 40 and then held a steady increase trends. Meanwhile 46.15% of loci showed high frequency allele. The results indicate that cultured population show predominant alleles in most loci because of selection pressure. Due to many homozygosity, the change of effect allele numbers, expected heterozygosity and polymorphism information content are little when the sample size is more than 40. In addition, the number of microsatellite markers and polymorhphism level also have a little effect on the estimation of population genetic structure. So, we suggested that the numbers of markers is more than 20 and sample size is 40 to 50 when using microsatellite markers to estimate population genetic structure.