Hard clam is an important cultured species in Taiwan. The purpose of this research is to establish the genotyping technology of clams. To establish the genotyping method, we must make sure the genome extraction quality and the stable, repeatable RAPD genotyping technology. In this study, we collected clams from different regions of Taiwan (Wild clams: Matsu, Danshui River and Longmen, cultured clams: Beimen and Keelung Market) as materials. After inspecting 50 sets of amplified bands of RAPD primers, we selected 6 of them for subsequent analysis as follow-up analysis. These 6 sets of primers could amplify a total of 93 bands, of which 46 polymorphic bands can be analyzed. Using UPGMA (Unweighted Pair Group Method with Arithmetic Mean) for cluster analysis can divide 76 individuals into three groups. The samples were divided into three groups as the genetic similarity was 0.56, one is Matsu and Danshui river wild clams, the other is 3 Matsu wild clams, and the last group was from the market. Further analysis by Neighbor-Joining (NJ), the samples can be divided into two groups, one group was wild clams (Matsu, Longmen, and Danshui river), and the other was farmed clams (market clams and Beimen clams). Genotyping technology can identify the geographic group of Clams. And it can provide a reference for future breeding to reduce the genetic divergence caused by the closeness of the breeding parents.