The common reactions of dioxygen, superoxide and hydroperoxides with thiolates are thought to proceed via persulfenate intermediates, yet these have never been visualized. Here we report a 1.4 Å resolution crystal structure of the Fe2+-dependent enzyme cysteine dioxygenase (CDO) containing this putative intermediate trapped in its active site pocket. The complex raises the possibility that, distinct from known dioxygenases and proposed CDO mechanisms, the Fe-proximal oxygen atom may be involved in the primary oxidation event to yield a unique three-membered Fe-S-O cyclic intermediate. A non-polar environment of the distal oxygen would facilitate isomerization of the persulfenate to the sulfinate product.