Nitrogen fixing Azotobacter vinelandii has two [2Fe-2S] proteins, FeSI and FeSII, Shethna protein I and II. In this study, we present the 2.11 Å, and 2.34 Å resolution X-ray crystal structures of FeSI and FeSII, respectively. FeSII has been shown as a protective enzyme for nitrogenase against oxygen-mediated inactivation. However, there is no known relation of A. vinelandii FeSI with nitrogenase, even though it is homologous to the [2Fe-2S] ferredoxin from Clostridium pasteurianum, which has been shown to interact with the nitrogenase MoFe protein. FeSI reveals a homodimer with [2Fe-2S] cluster coordinated by the side chains of surrounding conserved cysteine residues. It is highly similar to the structure of [2Fe-2S] protein from Aquifex aeolicus, including the positions of [2Fe-2S] clusters and conserved cysteine residues. On the other hand, dimeric FeSII reveals five monomers per asymmetric unit. All four copies are in an “open” conformation which may allow the [2Fe-2S] cluster to interact with nitrogenase, whereas one copy is in a “close” conformation which has a less accessible [2Fe-2S] cluster. The conformational changes may be related to oxidation and reduction states of the [2Fe-2S] cluster. These structures will provide crucial information for understanding the nitrogenase oxygen protection mechanism, and elucidating of the relations of iron-sulphur proteins in both structural and evolutionary aspects.