Taking the V4region of 18S rDNA as the target gene, we designed the primer V4 (F/R) and adopted high-throughput sequencing technology to evaluate the diversity and relative abundance of the eukaryotic phytoplankton community in different seasons of the year 2014 in Liaodong Bay. The results showed that there were 29 toxic algae in Liaodong Bay, including 8kinds of paralytic shellfish poisoning (PSP) algae, 2kinds of diarrhetic shellfish poisoning (DSP) algae, 3kinds of yessotoxic (YTX) algae, 2kinds of neurotoxic shellfish poisoning (NSP) algae, 13kinds of hemolysin, and a kind of exopolysaccharide (EPS) algae. Of these, 19toxic algae were reported to have caused either red or brown tides. Eight of the toxic algae, most of which belonged to Dinophyta, were capable of causing large-scale fish deaths. We found 18algal species that had been previously undetected or unreported in Liaodong Bay, in which 9algal species even had not previously appeared in other Chinese waters. The algal species had different trophic modes, including 8kinds of autotrophs, 20kinds of mixotrophs, and a kind of heterotroph. There were high risks from PSP, YTX, and NSP in summer;high risks from NSP in autumn; high risks from DSP in spring and summer; and the eastern and western waters of Liaodong Bay were prone to shellfish toxicity disasters. During spring, the water temperature was significantly and negatively correlated with the biomass of YTX and NSP algae. During summer, some environmental factors, such as chemical oxygen demand, oil, dissolved inorganic nitrogen (DIN), lead, and cadmium, were significantly and positively correlated with toxin-producing algae, but zinc, arsenic, oil, and DIN were positively correlated with toxic algae in the winter. The environmental factors were not significantly correlated with toxic algae in the autumn. The correlations between toxic algae and environmental factors should be further explored.