The increasing global consumption of seafood has led to increased trade among nations, accompanied by mislabeling and fraudulent practices that have rendered authentication crucial. The multi-isotope ratio analysis is considered as applicable tool for evaluating geographical authentications but requires information and experience to select target elements such as isotopes, through a distinction method based on differences in habitat and physiology due to origin. The present study examined recombination conditions of multi-elements that facilitated geographically distinct classifications of the clams to sort out appropriate elements. Briefly, linear discriminant analysis (LDA) analysis was performed according to several combinations of five stable isotopes (carbon (δ13C), nitrogen (δ15N), oxygen (δ18O), hydrogen (δD), and sulfur (δ34S)) and two radiogenic elements (strontium (87Sr/86Sr) and neodymium (143Nd/144Nd)), and the geographical classification results of the Manila clam Ruditapes philippinarum from Democratic People’s Republic of Korea (DPR Korea), Korea and China were compared. In conclusion, linear discriminant analysis (LDA) with at least four elements (C, N, O, and S) including S revealed a remarkable cluster distribution of the clams. These findings expanded the application of systematic multi-elements analyses, including stable and radiogenic isotopes, to trace the origins of R. philippinarum collected from the Korea, China, and DPR Korea