Polyunsaturated fatty acids (PUFAs) are fatty acids with more than one double bond in the chemical structure. Arachidonic acid (ARA, 20:4 (n-6)) and eicosapentaenoic acid (EPA, 22:5 (n-3)) are common PUFAs with beneficial health effects. Marine fish and meat are the main sources of omega-3 and omega-6 fatty acids in human's diet, respectively. In particular, there is a general decline in fish catch, implicating the need for an alternative source of omega-3 fatty acids. Previous studies have examined the production of polyunsaturated fatty acids including ARA and EPA by various microorganisms, including microalgae, fungi, and thraustochytrids. In this study, the production of ARA and EPA by 10 isolates of four estuarine Halophytophthora species (Halophytophthora avicenniae, Halophytophthora polymorphica, Halophytophthora vesicula, and Halophytophthora spinosa var. spinosa) cultured from fallen mangrove leaves in Taiwan was examined. The yield of ARA ranged from 0.004 to 0.052 g/L with the highest yield of ARA obtained from H. spinosa var. spinosa IMB162, but no or a very low level of EPA was produced by IMB162. For EPA production by Halophytophthora spp., the yield ranged from 0 to 0.047 g/L. Percentage of ARA in total fatty acid ranged between 7.16 and 25.02%. One-way ANOVA analysis using Tukey Test (p ≥ 0.05) suggested that there is significant difference in the percentage of EPA in total fatty acid produced by the isolates, which ranged from 0.01 to 18.42%. BODIPY 505/515 fluorescent staining suggests that lipid bodies were evenly distributed in the mycelia of Halophytophthora species.