Abstract: 8 polymorphic microsatellite loci were selected for parentage determination on different shell color lines of Patinopecten yessoensis. 3 full-sib families and 1 half-sib family of P. yessoensis, each with 40 individuals, their parents were subjected to microsatellite analysis. The value of the total exclusionary power of 8 loci was 0.823 with the parents were unknown; when a typed single parent was known, the value of the total exclusionary power of 8 loci was 0.961. Two methods were used to analyze the parentage determination of all the offspring. The method 1: when only the genotype data of parents and progeny were known, the values of LOD of candidate parents were gained by CERVUS 2.0, and then two parents with the maximum LOD values were directly considered as the candidate parents. The method 2: when the values of every candidate parent of offspring as method 1 were calculated, the one with the maximum value of LOD was considered to the first candidate parent. In the condition that the first candidate was treated as a known parent, the LOD values of candidate parents of offspring were recalculated by CERVUS 2.0. The second candidate parent of every offspring was finally gained through selecting the candidate parents with maximum value of LOD again. The results showed that the accuracy rate exceeded 95% by the method 2, which suggested that the method 2 was suitable for the parentage identification of different shell color lines of Japanese scallop. As the null alleles were observed at the two loci of all the microsatellite loci from family F1 and F2, and which would lead to mismatch of the offspring and parents, two kinds of genotype files including the null alleles existing ones (situation 1) and the null alleles lost ones (situation 2) were used for the parentage analysis. The results suggested that there was no significant difference in the success rate of paternity testing in two situations, which revealed that the analysis for the value on LOD of candidate parents gained by some microsatellite loci would reduce the error occurred in parentage determination on the different shell color lines of P. yessoensis. Based on these results, it was concluded that the technique of microsatellite marker was competent for the task for parentage analysis of different shell color lines of P. yessoensis.