Microalgae represent a unique experimental system to study stress responses of photosynthetic organisms. In higher plants, response and adaptation to stress takes place in two levels: The metabolic level and the morphological/structural level. In many cases it is difficult, if not impossible, to determine which is the initial response and which one is just a result of the initial modification. Since microalgae lack the morphological structure that characterizes higher plants they may be used as a unique experimental system to study metabolic and molecular processes associated with the response and adaptation of photosynthetic organisms to stress. The study of stress physiology and acclimation of microalgae also has an important application in further development of the biotechnology for mass culturing of microalgae: 1) When culturing algal cells under outdoor conditions cells are exposed to severe changes in light and temperature much faster than the timescale required for the cells to be able acclimate. A better understanding of those parameters and the ability to monitor those conditions will provide the growers with a better knowledge on how to optimize growth and productivity; 2) Induction of accumulation of high value products is associated with stress conditions. A better understanding of the physiological response may help in providing a better production system for the desired product and at a later stage give an insight of the potential for genetic modification of desired strains; 3) The potential use of microalgae as part of a biological system for bioremidation/detoxification and waste treatment is also associated with growing the cells under stress conditions; 4) Microalgae represent a promising alternative to convert CO2 into high added value products and biofluels. Algae biorefineries may thus alleviate food versus fluel conflicts and may become particularly advantageous for regions with limited biomass availability and land unusable for agriculture. Understanding the process associated with these unique environmental conditions may help in choosing the right culture conditions as well as selecting strains in order to improve the efficiency of the biological process.