Although production of ROS and cell mortality were not directly measured in this study, multiple lines of evidence suggest that the motile cells suffered more severe photo-oxidative stress than palmella cells when exposed to HL. First, more profound decreases in the quantum yields of PSII, D1 protein, and PsbO, as well as in several chloroplast membrane lipids occurred in motile cells than in palmella cells under HL. In TWS119 oxygenic photosynthetic organisms, PSII and PSI are two major sites of ROS production. ROS produced at PSII and PSI can damage proteins, lipids, and pigments, especially D1 protein at PSII and lipids containing polyunsaturated fatty acids. Second, pronounced astaxanthin accumulation in motile cells is an indication of severe photooxidative stress induced under HL. Although astaxanthin can react with ROS and astaxanthin synthesis consumes molecular oxygen—the precursor of ROS—a higher astaxanthin content in motile cells than in palmella cells reflects a greater stress on motile cells exposed to HL. Consequently, motile cells may die off more quickly than cells with lesser amounts of astaxanthin; this was confirmed by our previous study in which H. pluvialis cells exposed to higher irradiance accumulated more astaxanthin but exhibited higher cell mortality. Diacylglycerol-based polar lipids are the building blocks of the cellular membranes of living organisms. It is generally believed that glycolipids and the phospholipid PG are the major components of chloroplast thylakoid membranes, whereas phospholipids like PE, PC, PI, and the nonphosphorus betaine lipid DGTS reside in the extraplastidic membranes of photosynthetic cells. Our results indicate that the major classes of chloroplast membrane lipids exhibit different fates under HL stress in H. pluvialis. PG showed the most profound decrease among all the chloroplast membrane lipids in both motile and palmella cells; MGDG was dramatically reduced in motile cells and red cysts under HL; by contrast, DGDG and SQDG showed moderate decreases in both motile and palmella cells under the same conditions. The different responses of these lipids may result from their uneven distributions among the photosynthetic complexes and their distinct functional roles in maintaining the proper structure and function of chloroplast membranes. Palmella cells can develop a suite of protective mechanisms during encystment to bestow greater resistance to HL than motile cells, and thus, applying palmella cells instead of motile cells to the stressful red stage of cultivation may represent a promising strategy for increasing growth and astaxanthin production. During the first day under HL, astaxanthin productivity in palmella cells was less than in motile cells. From a biotechnical perspective, high astaxanthin contents are desirable, although higher yields can be achieved be extending culturing time.