Reproductive success of released animals becomes a growing interest in the context of stock enhancement program and conservation biology. In the case of the Ezo abalone (Pacific abalone; Haliotis discus hannai), limited information is available about the extent of interbreeding between natural and released hatchery populations. This study aimed to develop microsatellite DNA markers from Ezo abalone to address the issue. We developed 38 microsatellite markers that worked well in three full-sib families established from wild caught abalone. Of these, nine markers, with which alleles could be scored easily and accurately, were applied to two population samples derived from coastal areas where intensive releases of hatchery-produced abalone seedlings have been carried out. Multilocus estimates of genetic population differentiation calculated based on the nine markers ( F ST analogue θ and R ST analogue ρ) rejected a null hypothesis of genetic homogeneity between the populations ( θ=0.048, P<0.00001; ρ=0.029, P=0.0051). Although both populations conformed to Hardy Weinberg's equilibrium at almost all of the nine loci, the results of simulation analysis for variance of relatedness coefficient provided evidence of nonrandom mating in each population, possibly caused by the cumulative effect of stocking on the genetic make-up. The population analysis presented here is preliminary; but we consider that the microsatellite markers are potentially an efficient means to examine the reproductive contribution of released abalone to natural resources.