Carbon monoxide dehydrogenases (CODHs) catalyze the reversible oxidation of carbon monoxide with water to carbon dioxide, two protons, and two electrons. The CODHs of anaerobic microorganisms harbor a complex Ni/Fe/S-containing metal center called a C-cluster in their active site, which activates the substrates water and carbon monoxide, stabilizes an intermediary metal-carboxylate, and transiently stores the two electrons generated in the reaction. Several small molecules have been reported to inhibit carbon monoxide oxidation by CONS, among which the cyanide anion acts as a slow binding inhibitor. Cyanide is isoelectronic to the substrate carbon monoxide, and its binding to the C-cluster has been reported to involve nickel, nickel and iron, or only iron. We report the crystal structure of CODH-II from Carboxydothermus hydrogenoformans in complex with cyanide at 1.36 angstrom resolution. The structure reveals that cyanide binds to the C-cluster at an open coordination site completing the square-planar coordination geometry of the nickel ion. White active CON has a water/hydroxo-ligand bound to an iron ion near nickel, in the cyanide complex the water/hydroxo-ligand is lost and iron occupies a position more close to the nickel ion. Based on the structure, we suggest that the competitive inhibitory character of cyanide originates from it obstruction of carbon monoxide binding to the nickel ion while the slow binding inhibition is due to a conformational change of the protein during which the water/hydroxo-ligand bound to iron is lost.