The present study reports the changes in the phytoplankton community structure in Taklong Island National Marine Reserve (TINMAR), Guimaras Island, Philippines. Quantification of PAH yielded undetectable results, whereas, primary productivity, phytoplankton density, and diversity values were higher as compared to samples before the oil spill and samples from the reference site. Sixty-nine genera representing 6 classes of phytoplankton were identified. Class distribution revealed that diatoms belonging to Coscinodiscophyceae, Bacillariophyceae and Fragilariophyceae were dominant in the area. Class Coscinodiscophyceae was the best represented class with 1,535 individuals/L seawater. The top-ranked diatom genera encountered were Chaetoceros, Skeletonema, Thalassionema, Rhizosolenia, and Bacteriastrum. The shifts in dominance of diatoms over dinoflagellates and fast-growing centric diatoms over pennate diatoms are indicative of a stressed phytoplankton community. Both the Simpsons (1/D’) and Shannon-Weiner (H’) values registered for the 2006 TINMAR samples (1/D’:11.23; H’:1.304) were higher than those obtained from pre-oil impacted samples (1/D’:8.83; H’:1.07) and samples from the reference site (1/D’:8.798; H’:1.039). The present findings provided information on the direct impact of a recent oil spill on phytoplankton community and demonstrate the suitability of using phytoplankton as bioindicators of environmental stress.