<p>Since 1983, San Pedro Bay in the Philippines had been reported to be the site of episodic <em>Pyrodinium bahamense </em>var. <em>compressum</em> blooms that cause paralytic shellfish poisoning in its nearby coastal communities. This bay is also subjected to numerous typhoons, the strongest of which was super typhoon Haiyan in November 8, 2013.<strong> </strong>Phytoplankton ecology of this bay must have unique characteristics. For the first time, the seasonal dynamics of potentially toxic and harmful phytoplankton in this bay is elucidated. This is also the first record of a bloom of the cyanobacteria, <em>Trichodesmium erythraeum</em> that reached 90,000 cells/L in April 2013. There were 19 other potentially toxic and harmful phytoplankton encountered during the sampling period. This consisted of a haptophyte, <em>Phaeocystis globosa, </em>the diatom <em>Pseudo-nitzschia</em> and 17 dinoflagellates. Seven of these harmful algae had densities high enough to be traced through time.<strong> </strong>Normally, diatoms abound during the dry season. But here, <em>Pseudo-nitzschia </em>increased in abundance during the wet season of 2012 and 2013. The dinoflagellates behaved as expected and exhibited a relative increase in cell density during the rainy season of both years. <em>Phaeocystis globosa</em> also increased during the wet season. High nutrient availability during this season must have influenced the behavior of the phytoplankton despite differences in temperature and light intensity among seasons. Other notable but rare harmful species found only in plankton net tows during the study were <em>Pyrodinium bahamense </em>var. <em>compressum, Alexandrium tamiyavanichii</em>, <em>Cochlodinium</em> <em>polykrikoides, </em>and <em>Noctiluca scintillans. </em> <strong></strong></p>