The last decade period has been characterized by a remarkable increase in the need for food, bioenergy, and pharmaceutical compounds. Meanwhile, microalgae have been in the center of interest as a rich and sustainable source of highly valuable natural products and bioactive compounds. In this perspective, the present study aimed at investigating the biochemical composition of 10 cyanobacterial strains collected from several Tunisian inland waters, seeking to identify the possible use of cyanobacteria in nutraceuticals and pharmaceuticals industry, and for animal and human consumption. Ten local strains of cyanobacteria were isolated from several Tunisian inland waters and cultured in controlled laboratory conditions. Fatty Acid methyl esters were analyzed in each strain by Gas chromatography-Mass spectrometry (GC-MS) as well as total proteins, carbohydrates and different phycobiliproteins (phycocyanin, allophycocyanin and phycoerythrin). Results showed that Planktothrix agardhii, Leptolyngbya sp1., and Leptolyngbya sp2. contained 14 different fatty acids, among which oleic acid was the most abundant. These might be important in nutraceutical and agronomic sectors due to the potent antioxidant and larvicidal activities of oleic acid. Cylindrospermopsis raciborskii presents extraordinarily high levels of phycocyanin, making it an exceptional natural reservoir of effective and non-toxic drugs that are of particular interest against cancer and neurodegenerative diseases. Extracts from cyanobacterial strains represent a natural and available source of proteins, of highly valuable fatty acids, and especially of phycocyanin which is known by its extremely health beneficial properties. The nutritional and functional complements provided by these extracts can be used in the prevention of various diseases and also as effective and environmentally friendly insecticides.