This study aimed to develop a genetic analysis method to identify the origin of cockles (Tegilarca granosa). Initially, analysis of the mitochondrial COI gene revealed genetic variations among Korean, Chinese, and Japanese cockles. While distinguishing between Chinese and Japanese cockles was challenging, a specific haplotype (H1) found only in Korean cockles allowed researchers to infer their origin. Next, we analyzed the genetic characteristics of cockle populations using 19 microsatellite markers. This analysis validated the accuracy of assigning a cockle's origin and assessed the reliability of this method. The analysis revealed that three genetic loci (Teg02, Teg08, TMP18) displayed differing numbers of alternative alleles expressed between domestic populations and Chinese and Japanese populations, indicating genetic differentiation due to geographic separation. Using 16 microsatellite markers, the accuracy and reliability of origin determination achieved 89.6% and 86.6%, respectively. This shows there's enough information to distinguish between Korean, Chinese, and Japanese cockles. The results of this study demonstrate the usefulness of genetic analysis methods in determining the origin of cockles. This method is expected to contribute significantly to ensuring the safety and quality management of cockle distribution in the future. Additionally, there is a need for continued research to improve the accuracy and ability to differentiate origins through further development of microsatellite marker-based methods.