Microsatellite markers have been used for more than ten years to elucidate parentage relationships in aquaculture species. This study aimed to assess the feasibility of utilizing microsatellite markers for parentage determination in cuttlefish (Sepiella japonica) using simulations and real data analysis. We developed a panel of eight microsatellite markers in our lab. These markers were highly polymorphic with a mean of 10.1 alleles and an average expected heterozygosity value of 0.809. Using five simple sequence repeat markers, an allele frequency data-based simulation indicated that the combined exclusion probability values would be over 99%, whereas the rate of assignment success for the real data set was 91.8%. Mismatches caused by null alleles and scoring errors at microsatellite loci were the major reasons for the discrepancies between the simulations and real data analysis. We concluded that microsatellite markers can be used as a powerful tool to evaluate the effectiveness of enhancement and release programs for S. japonica.
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