In order to reveal the influence of stock size on the genetic structure of f ilial populations, two groups of Haliotis discus hannai ( SS with small number of parents, LS with large number of parents) were analyzed using AFLP( amplif ied fragment length polymorphism) markers. It was found the total number of loci in SS was less than that in LS and some rare loci of LS were lost in SS, Furthermore, the number of low-frequency loci increased, and high-frequency loci slightly decreased in SS compared w ith LS. The similarity was lower and heterozygosity was higher in SS than in LS. In order to prove above results, another two groups ( SH, LH) were also analyzed, which were hybrids of H . discus hannai @ H . discus discus. The trends of loci number, loci f requency, similarity and heterozygote in SH and LH were similar to SS and LS. Both results revealed small parental stock size could result in the loss of low-frequency loci and cause low-frequency loci to drift to highf requency loci, and extremely small stock size could result in temporal increase of heterozygosity.