Clean fuels are the critical requirement for industrialized world to combat emission of greenhouse gas. Hydrogen is one of the cleanest fuels that generates water as a result of combustion. Production of hydrogen from renewable and nonpolluting resources is an imperative task for sustainable clean fuel production. Biological processes provide an opportunity to produce hydrogen from renewable and economical bio-resources like biomass and solar energy through various processes such as direct/indirect photolysis, photo-fermentation, dark-fermentation, and CO gas-fermentation. This paper provides a comprehensive review on biological hydrogen production including organisms, type of substrates and their concentrations, role of chemical addition, operation conditions such as temperature, pH, and agitation, as well as illumination systems in case of light dependent processes. Further discussions in this work comprise various configuration of integrated biological processes of photolysis, dark, and photo-fermentation such as two component and three-component systems. •Presentation of recent progresses on biological hydrogen production processes.•Discussion of challenges on applications of biological hydrogen routes.•Comparisons of various configurations of integrated biohydrogen generation systems.