The dinophyte Amphidomataceae includes the genera Azadinium and Amphidoma. Four of these species are known to produce azaspiracids, which are lipophilic phycotoxins accumulating in shellfish. The diversity and biogeography of Amphidomataceae is far from yet resolved. Here we performed a time series sampling of both water and sediments in the Taiwan Strait from Nov. 2018 to April 2021. Metabarcoding was performed to unveil the diversity of Amphidomataceae targeting internal transcribe spacer (ITS1) region, followed by quantitative PCR with modified primers for Azadinium poporum ribotypes. The diversity of Amphidomataceae was revealed from the water samples with the aid of ITS1 based molecular phylogeny. These include eight new Azadinium clades and six ZOTUs (zero–radius operational taxonomic units) grouping together with Amphidoma languida. Moreover, eleven known Azadinium species including three ribotypes of Az. poporum (A, B, C), two ribotypes of Az. spinosum (A, C) and Az. dexteroporum (A, B) each, were present. The latter two species (ribotypes) have not been reported in China before. Among these toxigenic species, Az. poporum is relevantly abundant whereas others are rare. The maximum of 209 cells L^-1 of Az. poporum ribotype A was detected nearby Quanzhou in Nov. 2018 and 172 cells L^-1 of Az. poporum ribotype B was detected in Apr. 2021. Metabarcoding on sediment samples only revealed Az. poporum ribotype B and C, and this was confirmed by strains obtained with sediment incubation experiments. Using qPCR about 0.2 cysts g^-1 of Az. poporum ribotype B were quantified in May 2019 but cysts of Az. poporum ribotype C were not detected. Our results suggest that metabarcoding targeting ITS1 region is powerful to uncover the diversity of harmful dinophytes. Our results also highlight the rich diversity of Amphidomataceae and risk potential of azaspiracids in the Taiwan Strait and surrounding waters.