The effect of varying concentrations of the nitrogen source on the growth kinetics, lipid accumulation, lipid and DHA productivity, and fatty acid composition of C. cohnii was elucidated. Growth of C. cohnii was in three distinct growth stages: cell growth, lipid accumulation and a final lipid turnover stage. Most of lipids were accumulated in lipid accumulation stage (48–120 h) though, slow growth rate was observed during this stage. NaNO3 supported significantly higher lipid content (26.9% of DCW), DHA content (0.99 g/L) and DHA yield (44.2 mg/g glucose) which were 2.5 to 3.3-folds higher than other N-sources. The maximum level of C16–C18 content (% TFA) was calculated as 43, 54 and 43% in lipid accumulation stage under low nitrogen (LN, 0.2 g/L), medium nitrogen (MN, 0.8 g/L) and high nitrogen (HN, 1.6 g/L) treatments, respectively. Cultures with LN, by down-regulating cell metabolism, trigger onset of lipogenic enzymes. Conversely, NAD+/NADP+-dependent isocitrate dehydrogenase (NAD+/NADP+-ICDH) were less active in LN than HN treatments which resulted in retardation of Kreb’s Cycle and thereby divert citrate into cytoplasm as substrate for ATP-citrate lyase (ACL). Thereby, ACL and fatty acid synthase (FAS) were most active in lipid accumulation stage at LN treatments. Glucose-6-phosphate dehydrogenase (G6PDH) was more active than malic enzyme (ME) in lipid accumulation stage and showed higher activities in NaNO3 than other N-sources. This represents that G6PDH contributes more NADPH than ME in C. cohnii. However, G6PDH and ME together seems to play a dual role in offering NADPH for lipid biosynthesis. This concept of ME together with G6PD in offering NADPH for lipogenesis might be novel in this alga and needed to be explored.