Microalgae are photosynthetic microorganisms that have generated increasing interest in recent years due to their potential applications. Their biological capacity to grow faster than higher plants and their ability to convert solar energy into biomass and other bioactive molecules, has led to the development of various culture systems in order to produce different high-value products with commercial interest. The industrialization of the microalgae cultivation process requires the introduction of standardized quality parameters. In order to obtain bioactive compounds with high added value at a commercial level, it is necessary to sustainably produce biomass at a large scale. Such a process would imply specific stress conditions, such as variation in temperature, light or pH. These environmental conditions would make it more difficult to maintain the viability of the culture and protect the yield and condition of the target molecules. The physiological and biochemical impact of these stress factors on the microalgae biomass can be potentially measured by the presence and activity of various biochemical indicators called biomarkers. This review presents an overview of the main techniques that exist for assessing the “quality” of microalgae cultures through quantification of cell viability and vitality by monitoring specific markers indicative of the status of the culture.