The production of toxic secondary metabolites by marine phytoplankton and their accumulation in molluscs and fish has ecosystem-wide and human health impacts. The potent neurotoxin saxitoxin and its analogs, which can cause paralytic shellfish poisoning, are produced by species of the dinoflagellate genus Alexandrium. These toxins can accumulate in filter-feeding molluscs, including commercially grown species of shellfish. A feeding experiment was designed to assess the use of quantitative polymerase chain reaction to detect a gene involved in saxitoxin biosynthesis (sxtA) in two commercial oyster stocks. Both diploid and triploid Crassostrea gigas were fed with toxic cultures of Alexandrium minutum over a period of 12 days to allow toxin accumulation. A barcoding gene specific to Alexandrium (ITS 5.8s rRNA) and the sxtA gene, domain 4, which is specific to the saxitoxin synthesis pathway, were assayed. Both targets were detected in oysters collected after 6 and 12 days feeding with A. minutum, and after 24 h of depuration during which the oysters were fed nontoxic microalgae only. The target genes were not detected in control oysters. These methods can be used as a relatively rapid and inexpensive screen that is indicative of the presence of saxitoxin-producing microalgae in shellfish.