The distribution of phytoplankton and its correlation with environmental factors were studied monthly duringAugust 2012 to July 2013 in the Yantian Bay. A total of 147 taxa of phytoplankton were identified, and the averageabundance was in the range of 0.57×104 to 7.73×104 cell/L. A total of 19 species dominated the phytoplanktonassemblages, and several species that are widely reported to be responsible for microalgae blooms were theabsolutely dominant species, such as Skeletonema costatum, Navicula sp., Thalassionema nitzschioides,Pleurosigma sp., and Licmophora abbreviata. The monthly variabilities in phytoplankton abundance could beexplained by water temperature, dissolved oxygen, salinity, dissolved inorganic nitrogen (DIN), and suspendedsolids. The results of a redundancy analysis showed that pH and nutrients, including DIN and silicate (SiO4), werethe most important environmental factors controlling phytoplankton assemblages in specific months. It wasfound that nutrients and pH levels that were mainly influenced by mariculture played a vital role in influencingthe variation of phytoplankton assemblages in the Yantian Bay. Thus, a reduction of mariculture activities wouldbe an effective way to control microalgae blooms in an enclosed and intensively eutrophic bay.