The identification of core genes involved in the biosynthesis of saxitoxin (STX) offers a great opportunity to detect toxic algae associated with paralytic shellfish toxins (PST). In the Yellow Sea (YS) in China, both toxic and nontoxic Alexandrium species are present, which makes it a difficult issue to specifically monitor PST-producing toxic algae. In this study, a quantitative PCR (qPCR) assay targeting sxtA4, a domain in the sxt gene cluster that encodes a unique enzyme involved in STX biosynthesis, was applied to analyze samples collected from the YS in spring of 2012. The abundance of two toxic species within the Alexandrium tamarense species complex, i.e., A. fundyense and A. pacificum, was also determined with TaqMan-based qPCR assays, and PSTs in net-concentrated phytoplankton samples were analyzed with high-performance liquid chromatography coupled with a fluorescence detector. It was found that the distribution of the sxtA4 gene in the YS was consistent with the toxic algae and PSTs, and the quantitation results of sxtA4 correlated well with the abundance of the two toxic species (r ؍ 0.857). These results suggested that the two toxic species were major PST producers during the sampling season and that sxtA-based qPCR is a promising method to detect toxic algae associated with PSTs in the YS. The correlation between PST levels and sxtA-based qPCR results, however, was less significant (r ؍ 0.552), implying that sxtA-based qPCR is not accurate enough to reflect the toxicity of PSTproducing toxic algae. The combination of an sxtA-based qPCR assay and chemical means might be a promising method for monitoring toxic algal blooms. S axitoxin (STX) and its analogues, commonly known as paralytic shellfish toxins (PSTs), are potent neurotoxic alkaloids (1) synthesized by marine dinoflagellates in the genera Alexandrium, Gymnodinium, and Pyrodinium (2-4) and some cyanobacteria in freshwater (5-7). PSTs ingested by humans via shellfish vectors can reversibly bind to voltage-gated Na ϩ channels and inhibit the flow of sodium ions (1, 8), which leads to paralytic poisoning symptoms, including neurological numbness, tingling and burning of the lips and skin, ataxia, and fever. Severe poisoning may lead to a loss of muscular coordination and respiratory distress, which can be fatal (9).The biosynthetic pathway for STX, a compound with a complex chemical structure, remained a mystery for a long time prior to the identification of the STX synthesis genes in several cyanobacterial species (10). The identification and characterization of this set of core genes involved in STX synthesis provided the possibility of distinguishing the toxic potential of incipient blooms. A variety of genes related to toxin synthesis in cyanobacteria have been applied successfully not only in the detection, differentiation, and quantification of toxic cyanobacteria but also in studies on the regulation of toxin biosynthesis (7,(11)(12)(13)(14). In contrast, the genetic basis for STX production in dinoflagellates remains elusive, due to...