Understanding the dynamics and production of phytoplankton may contribute to the elucidation of the status of fishery resources and may be the key for better fisheries management since phytoplankton is at the base of the food chain. The changes and succession of phytoplankton community structure in Manila Bay was studied by conducting hydrobiological survey every other month from January 2012 to November 2015. It was determined from this study that diatoms dominated the phytoplankton composition all throughout the survey period and the total phytoplankton density was generally highest during southwest monsoons. Dinoflagellates and cyanobacteria, on the other hand, were relatively most dense during tradewinds. Although causative species for harmful algal blooms and fish kills were present, only the bloom of red Noctiluca scintillans was observed in January 2014 albeit no harmful implication to consumers was reported. Phytoplankton typically converged in the coasts of the bay, particularly at the eastern portion, but it is noteworthy to say that the sporadic pattern seen maybe attributed to the presence of their predators. The dramatic drop in the phytoplankton densities seem to coincide with the spawning of Sardinella fimbriata and Sardinella gibbosa.