Dioxotetrafluoromolybdate, (NH(4))(2)MoO(2)F(4), was synthesized in a single-crystal form and its structures [(I) at 297 K and (II) at 223 K] were determined by X-ray diffraction. Two independent states of a cis-MoO(2)F(4) octahedron are characteristic of static and dynamic disorder in structure (I). The dynamically disordered Mo atom is displaced from the symmetry axis producing four possible orientations of an anion that allow O and F atoms to be identified in separate orientations owing to the inherent differences between the Mo-O and Mo-F bonding. After the phase transition at lower temperature, (I) transforms into the statically disordered structure (II) with three possible orientations of the cis-MoO(2)F(4) octahedron. In this case, it also seemed possible to distinguish between O and F atoms on a local scale. H atoms of two independent NH(4) groups in (II) which form bifurcated N-H...F(O) hydrogen bonds were localized.