The rapid growth of global energy demand accelerates the development of sustainable, clean, and renewable energy sources. Biohydrogen production, driven by functional microorganisms, offers a promising solution. Multiple species of bacteria, fungi, microalgae, and archaea were able to produce hydrogen. This study reviewed the typical strains, together with their hydrogen-production mechanisms, e.g., bio-photolysis, photo fermentation, and dark fermentation. Bacteria (e.g., purple non-sulfur bacteria) and microalgae (e.g., cyanobacteria) have been widely investigated, with respect to the limited fungi and archaea. It showed that temperature, pH, and substrate availability could all substantially influence the efficiency of biohydrogen production. Meanwhile, photo and dark fermentations are favored for future possible industrial applications. Furthermore, this review summarized practical applications of biohydrogen production, such as applications of bioreactors, waste treatments, and integrated systems for hydrogen production, highlighting the importance of functional microorganisms in advancing biohydrogen technology under global energy crisis.