Harmful algal blooms (HABs) have occurred more frequently and emerged increasing hazard ways in recent years. This study firstly combined both short-read and long-read metabarcoding analyses for marine phytoplankton community and HAB species identification in the coastal waters of the Beibu Gulf. Short-read metabarcoding showed that the phytoplankton in the sea area had high levels of biodiversity, with Dinophyceae dominating, especially Gymnodiniales, and multiple small-size phytoplankton were also identified, which complements the previous lack of understanding phytoplankton of both small-size and those unstable after fixation. Of the top 20 phytoplankton genera identified, 15 were HAB-forming genera, which account for 47.3%-71.5% of the relative abundance of phytoplankton. Based on long-read metabarcoding it further revealed that 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. Contrast of the two metabarcoding methods 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 methods were quite different below the genus level. High abundance and diversity of HAB species were mainly due to the special life history and multiple nutritional modes, which provided a basis for preventing the potential impact of HAB species on the aquaculture and even nuclear power plants safety in the Beibu Gulf.