Abstract: Paralytic shellfish toxins(PSTs), including saxitoxin(STX) and its analogues, are potent neurotoxins produced by toxic dinoflagellates and cyanobacteria. Studies recently revealed a set of genes for STX synthesis in toxic cyanobacteria and dinoflagellates, and methods have been developed to quantitatively detect some core genes specific for toxin synthesis. In this study, a qPCR assay targeted to STX-synthetic gene sxtA4 was applied to detect PST-producing algae in the sea area adjacent to the Changjiang River estuary, which is the most significant region for recurring harmful algal blooms in China.Samples of toxic algae and PSTs collected along two transects in spring 2013 were measured with this method in parallel with two Taqman-based qPCR assays for Group I and IV of Alexandrium tamarense species complex and a HPLC method for PST determination. It was found that abundance of sxtA gene has a close relationship with that of A. tamarense species complex Group IV(r2=0.52, P0.05), suggesting that toxic A. tamarense species complex(Group IV)is the major PST producer during the sampling season in this region. However, no apparent relationship was found between PST level and the abundance of toxic algae derived from those qPCR assays. In conclusion, the sxtA-based qPCR assay has its advantages in monitoring PST-producing toxic bloom in the Changjiang River estuary, but it's not accurate enough to reflect PST level in the sea.