Eustigmatos cf. polyphem is a high mountain soil eustigmatophyte microalga. In this study, the growth and fatty acid and lipid accumulation in E. cf. polyphem under different nitrogen sources (NaNO3, NH4HCO3, and CO(NH2)(2)) and levels (3.6 and 6.0 mM nitrogen concentration) and light intensities (100 mu mol photons m(-2) s(-1) (low light, LL) and 300 mu mol photons m(-2) s(-1) (high light, HL)) were investigated in a column glass photobioreactor. Eustigmatos cf. polyphem accumulated total fatty acids (TFAs) and lipids at levels up to 51.83 and 63.41% of their dry weight, respectively, under 6.0 mM CO(NH2)(2)-nitrogen (N) and HL condition, which was also the optimal growth condition. Therefore, the maximum lipid productivity was 0.343 g L-1 day(-1), in which neutral lipids contributed 89.55% of the total lipids. Analysis of fatty acid compositions revealed that C16:0, C16:1, C18:1, and C20:5 were the main fatty acids, and the maximum content of C16:1 (palmitoleic acid) could reach 58.32% of the TFAs with a certain amount of eicosapentaenoic acid (EPA, C20:5, 2.41% of dry weight). Scale-up experiments conducted with different light path (LP) flat plate glass photobioreactors revealed that LP exerted a strong influence on the growth and lipid accumulation, with maximum lipid productivity of 0.142 g L-1 day(-1) obtained in cultures under 3.6 mM CO(NH2)(2)-N in a 3-cm LP photobioreactor. Overall, our results demonstrate that E. cf. polyphem is a promising microalga for biodiesel and nutraceutical production.