Microalgae-based biodiesel is increasingly recognized as an alternative to crop-based biodiesel. In this study, 10 local strains of dinoflagellates collected from Hong Kong waters, including a monoculture and field sample of Scrippsiella sp. isolated from an algal bloom, were evaluated against the performance of green alga Tetraselmis suecica. The specific growth rate, biomass production, lipid productivity, and fatty acid profile were investigated. The total lipid content of isolated strains ranged from 16.2% to 32.2% of the total dry biomass, whereas palmitic acid (C16:0) and docosahexaenoic acid (DHA, C22:6n3) were dominant in the fatty acid profile. Scrippsiella sp. has a high lipid productivity (47.3 mg/L/day) and fatty acid methyl esters (FAME) content (55.2–73 mg/g dry weight (dw)), which were comparable to that in green alga T. suecica. Further, monoculture and field sampled blooming Scrippsiella sp. showed no significant difference in most parameters, suggesting the possibility of harvesting a natural algal bloom population as a mitigation strategy to harmful algal bloom and to use as biodiesel feedstock. Overall, dinoflagellate species showed a slower growth rate (0.04–0.57 day−1) than most compared species (0.07–1.34 day−1), likely due to a large genome size and low chlorophyll to carbon ratio. Notably, most investigated dinoflagellates were not ideal for mass biodiesel production due to the low growth rate and lipid productivity. However, a high level of polyunsaturated fatty acids (PUFA) in dinoflagellates are prospective for further studies in other biotechnological applications. Though effectively harvesting algal blooming biomass can be complex, it can be further explored as a strategy for algal bloom mitigation and potentially creating values at the advantage of natural bloom when applying harvested biomass for biodiesel and bioactive compounds extraction.