Scallops, comprise more than 300 species identified in worldwide oceans, occupy an economically important position in many coastal countries. Until now, more than 15 scallop species have been considered as valuable fishery or aquaculture resources. Scallop adductor muscles are being considered as one of the most flavorful sea foods in markets at home and abroad, mainly due to their delicious taste and abundant nutrition. Because of the potential values, the scallop aquaculture has made great progress during the past three decades in many countries, especially in China. For examples, the farmed tideland for scallop aquaculture has exceeded 1 million hectares (ha.) and the annual production is more than 11 million tons in 2007, which makes China the firstrank not only in farmed acreage but also in annual production. However, with the blooming expansion of scallop aquaculture, some problems such as poor growth of some wild strains and largescale breakout of diseases have been arising during the past years. Further investigation and solution to these problems mainly depend on the availability of primary molecular genetic tools and the combination of efficient breeding programs with these molecular tools (i.e. molecular marker assisted selection, MAS). Microsatellite analysis based on polymerase chain reaction (PCR) offers the finest resolution for studying such genetic questions in aquacultural species. Based on the studies to date, microsatellite DNA marker has been one of the leading molecular markers for genetic analysis. Four scallops including Zhikong scallop Chlamys farreri, Noble scallop C. nobilis, Yesso scallop Patinopecten yessoensis and Bay scallop Argopecten irradians are the main species maricultured in China. In this study, we reviewed the progress in development of microsatellite DNA markers for these four scallops. We also summarized the applications of this robust molecular marker system in genetic analysis, such as genetic diversity analysis, pedigree reconstruction, genetic linkage map construction and species identification.