To gain an improved understanding of the mechanisms and species that drive brown tides, we used the V4region of 18S rDNA as the target gene to design the V4(F/R) primer and evaluated the diversity of the composition and relative abundances of the eukaryotic phytoplankton community in Liaodong Bay in different seasons with high-throughput sequencing technology. We found that some of the species in Liaodong Bay, such as Aureococcus anophagefferens, Ostreococcus tauri, Nannochloris sp., Nannochloropsis granulata, Micromonas pusilla, Pycnococcus provasolii, Chlorella vulgaris, and Chaetoceros calcitrans., had the potential to cause brown tides. Of these species, the risks were higher from Aureococcus anophagefferens and Nannochloropsis gaditana, which are distributed in the southwest and southeast of the bay, respectively. Aureococcus anophagefferens and Micromonas pusilla live with mixotrophs and other six potential brown tide species live with autotrophs.The abundance of Micromonas pusilla was the largest, with an average of 161445 ind/L, mainly occurring in autumn. Aureococcus anophagefferens and Ostreococcus tauri, with average abundances of 13912 and 13717 ind/L over the four seasons,respectively, mainly occurring in spring. Chlorella vulgaris and Chaetoceros calcitrans, with average abundances of 5498 and 5234 ind/L, respectively, were most abundant in autumn. Nannochloropsis gaditana. and Nannochloropsis granulata were absent in the winter and were present at only low abundances in other seasons. The correlations between the abundances of the brown tide species and environmental factors, such as the water temperature, water depth, N/P ratio, and inorganic nitrogen content, were significant. And the relationship between community structure succession and environmental factors need to be studied further.