Microalgae, as facultative aerobic organisms, convert solar energy to produce biohydrogen under anaerobic condition. Biohydrogen is a kind of ideal clean and renewable energy source with great commercial potential. Many endeavors have been focused on improving the biohydrogen yields by various means. Here, the research history of hydrogen production by microalgae (including cyanobacteria and green algae), the characteristics of nitrogenase and hydrogenase, the mechanisms of hydrogen production, the technological progress, and the application of enzymatic, genetic, and metabolic engineering methods to improve hydrogen production by microalgae are reviewed. In addition, the regulation of anaerobic metabolisms of Chlamydomonas reinhardtii after the disruption of key enzymes functioning in the fermentative pathways is discussed. Finally, the main challenges and obstacles facing the more efficient production and commercialization of hydrogen production from microalgae in the future are proposed.