Some dinoflagellate species within the genera Alexandrium, Gymnodinium and Pyrodinium are well-known producers of paralytic shellfish toxins (PST), which led to many poisoning incidents around the world. In the northern Yellow Sea, an important mariculture zone for scallop Patinopecten yessoensis, PST have been frequently detected from scallops. However, there is little knowledge concerning PST-producing microalgae in this region so far. In cruises carried out in 2011 and 2012, scallop and phytoplankton samples were collected from the northern Yellow Sea. PST were detected from scallops by high-performance liquid chromatography with fluorescence detection (HPLC-FLD). Toxin content and profile were remarkably different among the four tissues, i.e. viscera, adductor muscle, mantle and gonad, suggesting apparent toxin transfer and transformation in scallops. Viscera always had the highest content of PST dominated by low-potency N-sulfocarbamoyl toxins C1 and C2, which closely resembled the toxin profiles of net-concentrated phytoplankton samples in spring. Based on the morphological features, cells of Alexandrium spp. in net-concentrated phytoplankton samples were picked out and a partial sequence of the large subunit ribosomal RNA gene (LSU rDNA) was amplified using a single-cell polymerase chain reaction (PCR) method. Cells of both toxic A. tamarense species complex and non-toxic A. affine were identified from the phytoplankton samples based on the partial LSU rDNA sequence information. According to these findings, it is implied that A. tamarense species complex is the major toxic species related to PST contamination in scallops of the northern Yellow Sea. The presence of both toxic and non-toxic Alexandrium spp. in this region requires for a species-specific method to monitor the distribution and dynamics of A. tamarense species complex.