Hydrogen is a promising alternative to fossil fuel for a source of clean energy due to its high energy content. Some strains of phototrophic microorganisms are known as important object of scientific research and they are being explored to raise biohydrogen (BioH2) yield. BioH2 is still not commonly used in industrial area because of the low biomass yield and valuable down streaming process. This article deals with the methods of the hydrogen production with the help of two large groups of phototrophic microorganisms – microalgae and cyanobacteria. Microalgal hydrogen is environmentally friendly alternative to conventional fossil fuels. Algal biomass has been considered as an attractive raw source for hydrogen production. Genetic modified strains of cyanobacteria are used as a perspective object for obtaining hydrogen. The modern photobioreactors and outdoor air systems have been used to obtain the biomass used for hydrogen production. At present time a variety of immobilization matrices and methods are being examined for their suitability to make immobilized H2 producers. Display omitted •Hydrogen production from microalgae and cyanobacteria.•Mechanisms of biohydrogen metabolism.•Bioreactors for biohydrogen production process.•Enzymes of biohydrogen production.