Study on pedigree information and genetic diversity is essential for effective management of hatcheries. In this study we used six microsatellite loci for analysis of offspring parentage from two sets of brooders, to evaluate the genetic diversity and parental contribution in the production of progeny of Hypophthalmichthis molitrix. The effective number of alleles and the heterozygosity for parents and offspring was (3.63 and 4.38) and (0.943 and 0.960) for two groups, respectively. The contribution of the females and males to the offspring for the two groups was 61% and 91%, respectively. Females mated with 2–6 males, and males fertilized 2–5 females, revealing multiple paternity in this species. Our results revealed that the ratio of males to females plays an important role in parental contribution to offspring production. Despite a decrease in the heterozygosity among larvae towards their parents, the values obtained were still acceptable, which supports the hypothesis of genetic factors involves in mating patterns selected by parents to maintain the proper levels of heterozygosity in their progenies.