<jats:p>The dinoflagellate Alexandrium pacificum can produce paralytic shellfish toxins and is mainly distributed in the Pacific. Blooms of A. pacificum have been frequently reported in offshore areas of the East China Sea, but not along the coast. To investigate the bloom dynamics of A. pacificum and their potential origins in the Taiwan Strait, we performed intensive sampling of both water and sediments from 2017 to 2020. Ellipsoidal cysts were identified as A. pacificum and enumerated based on microscopic observation. Their abundances were quite low but there was a maximum of 9.6 cysts cm−3 in the sediment near the Minjiang River estuary in May 2020, consistent with the high cell abundance in the water column in this area. Cells of A. pacificum were examined using a quantitative polymerase chain reaction, and they appeared to be persistent in the water column across the seasons. High densities of A. pacificum (103 cells L−1) were observed near the Jiulongjiang and Minjiang River estuary in early May 2020, where high nutrients (dissolved inorganic nitrogen and phosphate), and relatively low temperatures (20–21 °C) were also recorded. Strains isolated from the East and South China Sea exhibited the highest division rate (0.63 and 0.93 divisions d−1) at 20 and 23 °C, respectively, but the strain from the Yellow Sea showed the highest division (0.40 divisions d−1) at 17–23 °C. Strains from the East and South China Sea shared similar toxin profiles dominated by the N-sulfocarbamoyl toxins C1/2, but the strain from the Yellow Sea predominantly produced the carbamoyl toxins GTX1/4 and no C1/2. Our results suggest that both cyst germination and persistent cells in the water column might contribute to the bloom formation in the Taiwan Strait. Our results also indicate that the East and South China Sea populations are connected genetically through similar toxin formation but separated from the Yellow Sea population geographically.</jats:p>