To investigate the relationship between lineage and its material properties in the Japanese scallop　population (Mizuhopecten yessoensis) in Saloma Lake in Hokkaido, Japan, we performed a lineage analysis based on sequence variation in the mitochondrial DNA segment (NcR2) and chemical analysis. Thirty five kinds of haplotype were detected by the lineage analysis in 240 samples of scallop and each haplotype was divided into four major groups, HG-001, (53%) , HG-004 (15%) , HG-012 (2l%) and HG-021 (11%). The analysis of material properties in these groups showed significant differences in soft tissue and gonad index, alanine and glutamic acid contents in the ligament as free amino acids.