Thraustochytrids are marine protists that can be abundantly found on fallen mangrove leaves. These organisms are drawing attention from scientists and commercial manufacturers alike primarily because they are able to produce omega-3 polyunsaturated fatty acids (PUFA) such as docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) in copious amounts within their cells. Scientists from Brazil, Malaysia, Taiwan, and Thailand have capitalized on their country’s thraustochytrids; yet, in the Philippines only a limited number of researches have been conducted on these organisms. Thus, the significance of this research is to further investigate, supplement additional information, and add to the number of existing studies on the thraustochytrids from Philippine mangroves. This research isolated, purified, and characterized thraustochytrids present in yellow, yellow brown, and brown leaves from two (2) mangrove species—Avicennia and Rhizophora spp. in Pagbilao Mangrove Forest. The thraustochytrids from each leaf sample of the two mangrove species were isolated and purified on GYPSA (Glucose Yeast Peptone Sea Salt Agar) media. Morphological characterization was done through microscopy for partial identification. The isolates present on fallen mangrove leaves from Pagbilao, Quezon were preliminarily identified as morphologically indicative to either be Aurantiochytrium, Hondaea, or Monorhizochytrium.