Mangroves create an ecological environment for a diverse assemblage of organisms, including marine and mangrove oomycetes. Halophytophthora spp., in particular, are isolated from fallen senescent mangrove leaves. Studies reported on Philippine oomycetes are mostly on their distribution and taxonomy; while fatty acid studies have not yet been fully explored. Recently, oomycetes were reported as efficient producers of various fatty acids, therefore, bioprospecting efforts are aimed at obtaining more industrially important fatty acid compounds for aquaculture, biodiesel production, and human consumption. In this study, 21 isolated oomycetes, identified as Halophytophthora spp., and 2 type-species of Phytopythium, were grown in a broth medium containing peptone, yeast extract, glucose, and 50% seawater incubated at room temperature for three weeks for fatty acid production and identification. Results revealed the presence of various fatty acids, mainly palmitic acid (C16:0), linoleic acid (C18:2n6c), and oleic acid (C18:1n9c) cis-11,14,17-eicosatrienoic acid (ETA, C20:3n3), and stearic acid (C18:0) from Halophytophthora and Phytopythium isolates ranging from 2–30% total fatty acids. An omega-6 fatty acid, Ƴ-linolenic acid (GLA, C18:3n6), was found in Phytopythium isolates with considerably higher concentrations compared to Halophytophthoras. Further, omega-3 polyunsaturated fatty acid, cis-11,14,17-eicosatrienoic acid (ETA, C20:3n3) were detected on most oomycete isolates.