TAG is a feedstock for the production of biofuels like biodiesel and bio–jet fuel, bioplastics, and other chemicals that are currently derived from fossil fuels. Moreover, because of its great growth potential and high photosynthetic efficiency, H. pluvialis is an alternative solution for removing CO2 from fossil-fired power plants. A two-stage cultivation strategy is often applied to mass culture of H. pluvialis. In the green stage, optimal light intensity and nutrient-replete media are provided to promote the growth of green vegetative cells; when the cell density reaches a maximal level, the culture is subjected to stress Tofacitinib conditions to induce astaxanthin biosynthesis and accumulation. At this red stage, many cells die off, while the surviving ones undergo profound biochemical and cellular changes, transforming the flagellates into red cysts. Although cell death is related to high light, high salinity, and other stressors, such as the application of acetate or Fe2+ to the cultures, the exact causes of cell death under stress remained largely unknown. The susceptibility of fast-growing H. pluvialis cells to adverse culture conditions leads to a substantial reduction in biomass productivity, a major obstacle that prevents expansion of the H. pluvialis industry. It has recently been observed that the H. pluvialis strain CCAP 34/12, which is dominated by flagellates at the exponential growth phase, was more susceptible to HL stress than another strain dominated by resting vegetative cells. These resting cells are also called palmella cells and are transformed from flagellates under favorable growing conditions. The death of flagellates under HL was attributed to the production of reactive oxygen species. Although a number of protective mechanisms contributing to the survival of SAG 34/1b under HL were identified, including down-regulation of linear photosynthetic electron transport and enhancement of the alternative plastid terminal oxidase pathway, it was unclear whether these mechanisms were developed during the cell transformation or resulted from different genetic makeups of the two Haematococcus strains. A recent comparative proteomic analysis of flagellates and resting cells from a single Haematococcus strain showed that a number of proteins involved in stress responses were induced in the resting cells but absent in the flagellates. The aim of this study was to determine the physiological and biochemical changes that occur during the transformation of motile flagellates into resting palmella cells and to dissect the key mechanisms by which the different forms of Haematococcus cells cope with HL. To gain more insight into the molecular–level changes in lipids that occur in response to HL, we developed a mass spectrometry–based lipidomics method for absolute quantification of glycerolipids. Our results suggest that introducing resting palmella from H. pluvialis.