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Food allergies are common disorders impacting the quality of human life and health costs, occurring in approximately 1–3% in adults 4–6% in children of the general population. Tropomyosin present in mollusk species is the most common allergen in humans and causes excessive immune responses. To simultaneously detect tropomyosin allergens in mollusk species, a multiplex PCR assay combined with capillary electrophoresis was developed for the detection of tropomyosin genes of oyster, mussel, abalone, and clam, and the 18S rRNA gene of eukaryotes.