From Wikepedia (http://en.wikipedia.org/wiki/Hydrogen):

“H2 is a product of some types of anaerobic metabolism and is produced by several microorganisms, usually via reactions catalyzed by iron- or nickel-containing enzymes called hydrogenases. These enzymes catalyze the reversible redox reaction between H2 and its component two protons and two electrons. Evolution of hydrogen gas occurs in the transfer of reducing equivalents produced during pyruvate fermentation to water.

Water splitting, in which water is decomposed into its component protons, electrons, and oxygen, occurs in the light reactions in all photosynthetic organisms. Some such organisms — including the alga Chlamydomonas reinhardtii and cyanobacteria — have evolved a second step in the dark reactions in which protons and electrons are reduced to form H2 gas by specialized hydrogenases in the chloroplast. Efforts have been undertaken to genetically modify cyanobacterial hydrogenases to efficiently synthesize H2 gas even in the presence of oxygen.

Other rarer but mechanistically interesting routes to H2 production also exist in nature. Nitrogenase produces approximately one equivalent of H2 for each equivalent of N2 reduced to ammonia. Some phosphatases reduce phosphite to H2.”