Simple SummaryMicrosatellite markers are widely used in genetic breeding and population genetic structure analysis. In this study, microsatellite markers are used to analyze the genetic diversity and population genetic structure ofMytilus unguiculatusin seven coastal areas of China. The results showed thatM.unguiculatushas high genetic diversity with genetic structure differences observed between the Qingdao population and the other six populations. The genetic structure ofM. unguiculatuis relatively weak. These findings provide a molecular biological basis for the rational development and protection of wild germplasm resources ofMytilus unguiculatusin China and can serve as a data reference for the formulation of reasonable breeding programs.AbstractThe hard-shelled musselMytilus unguiculatusplays an important role in mussel aquaculture in China due to its characteristic and nutritive value. In this study, 10 microsatellite loci are used to study the genetic diversity and genetic structure of seven location populations ofM. unguiculatusin coastal areas of China. The results of amplification and genotyping show that the observed heterozygosity (Ho) and the expected heterozygosity (He) are 0.61~0.71 and 0.72~0.83, respectively.M. unguiculatushas high genetic diversity. The inbreeding index (FIS) ofM. unguiculatusis significantly positive (FIS: 0.14~0.19), indicating that inbreeding might exist within populations. The genetic structure ofM. unguiculatusis weak within populations from the East China Sea All results showed that genetic differences existed between the Qingdao population from the Yellow Sea and other populations from the East China Sea. It does not detect a population bottleneck event or expansion event in the populations. The results from this study can be used to provide important insights in genetic management units and sustainable utilization ofM. unguiculatusresources and provide a better understand of genetic structure of marine bivalve with similar planktonic larval stage in the China Sea.