AbstractHarmful algal blooms (HABs) have occurred more frequently in recent years. In this study, to investigate their potential impact in the Beibu Gulf, short‐read and long‐read metabarcoding analyses were combined for annual marine phytoplankton community and HAB species identification. Short‐read metabarcoding showed a high level of phytoplankton biodiversity in this area, with Dinophyceae dominating, especially Gymnodiniales. Multiple small phytoplankton, including Prymnesiophyceae and Prasinophyceae, were also identified, which complements the previous lack of identifying small phytoplankton and those unstable after fixation. Of the top 20 phytoplankton genera identified, 15 were HAB‐forming genera, which accounted for 47.3%–71.5% of the relative abundance of phytoplankton. Based on long‐read metabarcoding, a total of 147 OTUs (PID > 97%) belonging to phytoplankton were identified at the species level, including 118 species. Among them, 37 species belonged to HAB‐forming species, and 98 species were reported for the first time in the Beibu Gulf. Contrasting the two metabarcoding approaches at the class level, they both showed a predominance of Dinophyceae, and both included high abundances of Bacillariophyceae, Prasinophyceae, and Prymnesiophyceae, but the relative contents of the classes varied. Notably, the results of the two metabarcoding approaches were quite different below the genus level. The high abundance and diversity of HAB species were probably due to their special life history and multiple nutritional modes. Annual HAB species variation revealed in this study provided a basis for evaluating their potential impact on aquaculture and even nuclear power plant safety in the Beibu Gulf.