The objective of this study was to develop an analytical method for protecting Jiaozhou Bay clam (Ruditapes philippinarum) with Protected Designation of Origin (PDO). The R. philippinarum samples were collected from three major producing areas (Jiaozhou Bay, Nantong coast, and Dalian coast) in China, and the Meretrix meretrix samples were from Nantong coast in May and September 2014. The contents of 46 elements in all clam samples were determined by inductively coupled plasma mass spectrometry. The obtained data were analyzed using analysis of variance, principal component analysis, and stepwise linear discriminant analysis. The results showed that both the geographical origin and season affected elemental contents in R. philippinarum. Seven elements (Mg, Cd, Sn, Sb, Cs, Ba, and U) independent of seasonal variation were selected as good indicators for discriminating the geographical origin of clams. Based on the discriminant models built with these seven elements, the predictions of the geographic origin gave an overall correct classification rate of 100.0 % and a cross-validation rate of 97.2 %. In addition, R. philippinarum and M. meretrix had their own elemental fingerprinting patterns and could be distinguished. Therefore, the multi-element analysis combined with multivariate statistics can be used for the identification of Jiaozhou Bay clam with PDO.