Hydrogenases are enzymes that can potentially be used in bioelectrical devices or for biological hydrogen production, the most studied of which are the [NiFe] type. Most [NiFe] hydrogenases are inactivated by oxygen and the few known O2-tolerant enzymes are hydrogen-uptake enzymes, unsuitable for hydrogen production, due to strong product inhibition. In contrast, the [NiFeSe] hydrogenases, where a selenocysteine is bound to the nickel, are very attractive alternatives because of their high hydrogen production activity and fast reactivation after O2 exposure. Here we report five high-resolution crystallographic 3D structures of the soluble form of the [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough in three different redox states (oxidized as-isolated, H2-reduced and air re-oxidized), which revealed the structural changes that take place at the active site during enzyme reduction and re-oxidation. The results provide new insights into the pathways of O2 inactivation in [NiFe], and in particular [NiFeSe], hydrogenases. In addition, they suggest that different enzymes may display different oxidized states upon exposure to O2, which are probably determined by the protein structure.