Microalgae have emerged as promising resources for highly unsaturated fatty acids. In this study, an indigenous microalga identified as Nannochloropsis oceanica CY2 was grown photoautotrophically to produce eicosapentaenoic acid (EPA; 20:5, n-3). Specific engineering strategies were employed to stimulate EPA accumulation in the microalgal cells. The results show that BG-11 was the most effective medium to grow N. oceanica CY2, giving an EPA content and biomass concentration of 2.38% (per dry cell weight) and 1.53 g/l. The EPA content nearly doubled when using the optimal nitrogen source (NaNO3) at a concentration of 1.50 g/l. The illumination system also markedly affected the EPA content for the photoautotrophic microalga. When the microalgal culture was illuminated with a red LED, an impressively high EPA content of 5.5% was obtained. Finally, using semi-batch cultures operations with LED-blue illumination, the EPA content of N. oceanica CY2 was stably maintained at 5.0%.