Three molybdenum(VI) cis-dioxo catalysts (8-10) were synthesized with the goal of developing stable and selective oxidation catalysts for sulfoxidation. Their reactivities were investigated with a variety of substrates. We have demonstrated the usefulness of these catalysts for the chemoselective sulfoxidation of sulfides in the presence of reactive moieties, which has important applications for total synthesis processes. Notably, these catalysts are able to oxidize compounds analogous to sulfur mustard and can be used as an alternative to sodium periodate or meta-chloroperoxybenzoic acid (m-CPBA) for the oxidation of various organic sulfides without sacrificing total conversion. As the catalysts are tolerant of water and hydrogen peroxide, they allow for the design of completely green oxidation reactions, particularly for sulfur-containing amino acids.