Nature has evolved three different ways of metabolizing hydrogen, represented by the anaerobic [Fe]-, [FeFe]- and [NiFe]-hydrogenases. Structural and functional studies of these enzymes have unveiled the unusual composition of their active sites and characterized their catalytic mechanisms. From a biotechnological viewpoint, the most interesting hydrogenases are those that contain a [NiFe] moiety in their active sites. Some of these enzymes are O2-resistant and can rapidly reductively recover from oxygen exposure whereas others are O2-tolerant and can oxidize H2 even at atmospheric oxygen levels. O2-resistant [NiFeSe]-hydrogenases have one of the Cys ligands of the active site replaced by a SeCys and do not display the hard-to-reactivate “unready” state provoked by O2. The reasons for this property might be related to the formation of O2-derived Se-O bonds, which are weaker than S-O bonds and, consequently, easier to break upon reduction. Conversely, membrane-bound O2-tolerant hydrogenases have an unusual proximal (relative to the active site) [Fe4S3] cluster coordinated by six Cys ligands. This cluster can rapidly send two successive electrons to the active site helping to reduce oxygen to water there. Some microorganisms posses more than one hydrogenase and use them in different ways. For instance, there are three well-characterized [NiFe]-hydrogenases in the model bacterium Escherichia coli. They are highly regulated and each one plays a specific role: microaerobic/anaerobic H2 uptake, anaerobic H2 evolution and, protection from O2-induced damage, respectively. These enzymes are discussed in connection with the metabolic changes E. coli undergoes during its transit through the intestinal tract of the host. O2-tolerant hydrogenases have been used to build bio-fuel cells that can function under air. Also, O2-resistant [NiFeSe]-hydrogenases have been attached to TiO2 particules for H2 production from solar energy. Hydrogenase active sites have also served as a source of inspiration for the synthesis of organometallic catalysts.