The first crystallographically characterized molybdenum(VI) selenoether complex [Mo2O4(OC3H6SeC3H6O)2] and its thioether analogue [Mo2O4(OC3H6SC3H6O)2] were synthesised. Their structural, electrochemical and oxygen atom transfer properties are compared. This is relevant for the molybdenum cofactors of the DMSO reductase family where the coordination of the active site metal occurs through O (serine/aspartate), S (cysteine) or Se (selenocysteine). Both structures are almost identical except for those parameters that are directly derived from the different sizes of the varied ligand atoms (Se and S). No trans influence was observed. The metal centered redox process (MoV↔MoVI) is at slightly lower voltage for the sulfur than for the selenium complex. The selenium compound catalyses the oxygen atom transfer from DMSO to PPh3 by a different mechanism and at a higher rate than the sulfur compound, which is an indication that cysteine and selenocysteine might be used for a purpose in the different molybdenum and tungsten cofactors.