Tropical microalgae and cyanobacteria have natural potential virtues that can be used in a wide range of bioproducts. Indeed, they represent a large biodiversity and benefit from favorable environmental conditions. In this context, 27 isolated marine tropical strains have been studied for their total lipid content, lipid class’s distribution and fatty acids composition. Their potential use for applications in the field of biodiesel and nutritional products has been evaluated by the determination of various parameters estimated in relation to the carbon chain size and the amount and/or position of double bonds in fatty acids (as example, the cetane number, the iodine value, the polyunsaturated/saturated acids ratio, the omega 6 and 3 ratio (n6/n3)). The dinoflagellates Prorocentrum lima and Amphidinium massartii, and the cyanobacteria Leptolyngbya sp. RS01 have good characteristics for biodiesel production whereas Spirulina sp. has a good profile of fatty acids for nutritional application.