Microalgae are photosynthetic microorganisms that have an extraordinary diversity which biotechnological potential is just beginning to be explored. Microalgae in biotechnology are presently the focus of an unprecedented surge in interest and investment worldwide. Understanding microalgal lipid accumulation under nitrogen starvation is of major interest for feedstocks, food and biofuel production. Although studies have been performed in model species, to this day it is critical to understand through particular mechanisms of biotechnological species. Tisochrysis lutea is traditionally used for aquaculture feed and presents advantages for lipid production. The wild type strain and a lipid over-accumulating selected mutant were used to perform the first comparative proteomic analysis about domesticated oleaginous micoalgae. 2-DE analysis was performed on two metabolic conditions for both strains and revealed significant differences in proteoms between the two strains and depending on nitrogen starvation. MS analysis allowed us to identify proteins. Four candidates were selected for their potential implication in lipid over accumulation during nitrogen starvation. They include proteins involved in biosynthesis of fatty acids, carbon homeostasis and carbohydrate catabolism. This proteomic study confirms the impacts of nitrogen starvation on global metabolism and provides insights on regulation of lipid metabolism in the oleaginous haptophyta Tisochrysis lutea.