Abstract <p>Assessment of the minimum number of microsatellite loci required for the primary analysis of population structure was performed using samples of the Japanese sea cucumber, <i>Apostichopus japonicus</i>. A total of ten microsatellite loci were used for the analysis as the maximum number. Based on the mean values of the allelic richness and <i>F</i>_st for each locus per all samples, markers with the minimum values of these criteria were removed one by one and Bayesian clusterization with determination of the parameters for calculation of the optimal number of groups was performed. It was shown that the genotypic distribution of individuals could be achieved with nine loci or more in the analysis if ranked on the basis of their allelic richness and differentiation power. Further effort is required to search for effective molecular markers that would allow the study of the population heterogeneity of the Japanese sea cucumber.</p>