The biotechnological usage of cyanobacteria as a source of clean fuel, vitamin C and bioactive compounds was investigated.  Five cyanobacterial strains were screened and tested for the potential of biodiesel production and the quality of biodiesel produced.  The inorganic nutritional value of the cyanobacterial strains was estimated through quantifying the strains' mineral content as well as vitamin C content.  To investigate the use of cyanobacteria as a source of bioactive secondary metabolites a phytochemical screening was conducted to test for the presence of alkaloids, flavenoids, saponins and tannins.  The different analyses indicated that Aphanizomenon sp., the heterocystous filamentous cyanobacterium contained highest lipid content, best biodiesel quality of more saturated and less unsaturated fatty acid composition, mineral content, vitamin C and most bioactive secondary metabolites.  As a confirmation of the ability of this cyanobacterium to produce secondary metabolites, degenerate primers were used to amplify genetic loci for secondary metabolites.  Multiple PCR products were obtained indicating that this isolate represents a rich bioactive compounds source.  The study thereby highlights the multiple biotechnological applications of cyanobacteria in general and Aphanizomenon in particular.