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Microalgae represent a new source of biomass for many applications. The advantage of microalgae over higher plants is their high productivities. The photoautotrophic microalgae include all photosynthetic microorganisms, i.e. Cyanobacteria (prokaryotes) or microalgae (eukaryotes). These microorganisms are characterized by a large biodiversity and chimiodiversity. Then, the analysis of microalgal and cyanobacterial biomass often needs specific adaptations of the classical protocols for extraction as well as for quantification of their contents. This chapter reviewed the main analytical methods used for the analysis of microalgae biomass and its main vaporizable compounds: proteins, polysaccharides, lipids, pigments and secondary metabolites.