The experimental design and techniques for biofuel production from different feedstock varies depending on geographical region, water sources (fresh water, sea water, waste water or brackish water) and overall, available species variations. Also the sampling, culture conditions, isolation, purification of cultures, harvesting, fatty acid extraction followed by conversion of extracted lipids to biofuel followed different methods in different studies. Therefore, it is a demand to simplify the techniques, improve the methods, and develop the efficiencies with less laborious inputs but rapid and best outcomes. Biofuel production research should focus not only selecting suitable biomass or obtaining high yield of lipids but also look for economically feasible method along with sufficient and continuous supply of biomass. Considering these, cyanobacteria and microalgae creates a great potential for biofuel production. In this review, we focused on compiling different materials and methods used for different studies and their best outputs towards biofuel production from cyanobacteria and micro-algae.