The solid solution series between Cu₂ZnSnSe₄, crystallizing in the kesterite type structure, and Cu₂MnSnSe₄, adopting the stannite type structure, i.e. Cu₂(Zn_1−xMn_x)SnSe₄, was studied by a combination of neutron and X-ray powder diffraction. Powder samples with 0 ≤ x ≤ 1 were synthesized by the solid state reaction of the pure elements and it was confirmed by wavelength-dispersive X-ray spectroscopy that each contained a homogeneous, off-stoichiometric quaternary phase. The lattice parameters and cation site occupancy factors were determined simultaneously by the Rietveld analysis of the neutron and X-ray powder diffraction data. The refined site occupancy factors were used to determine the average neutron scattering length of the cation sites in the crystal structure of the Cu₂(Zn_1−xMn_x)SnSe₄ mixed crystals, from which a cation distribution model was derived. For the end member Cu₂ZnSnSe₄, the disordered kesterite structure was confirmed and for Cu₂MnSnSe₄, the stannite structure was confirmed. The cross-over from the kesterite to stannite type structure by Zn²⁺ ↔ Mn²⁺ substitution in the Cu₂Zn_1−xMn_xSnSe₄ solid solution can be seen as a cation re-distribution process among the positions (0, 0, 0), (0, ½, ¼) and (0, ¼, ¾), including Cu⁺, Zn²⁺ and Mn²⁺. The Sn⁴⁺ cation does not take part in this process and remains on the 2b site. Moreover, the cross-over is also visible in the ratio of the lattice parameters c/(2a), showing a characteristic dependence on the chemical composition. The order parameter Q, the quantitative measure of Cu/B^II disorder (B^II = Zn and Mn), shows a distinct dependence on the Mn/(Mn + Zn) ratio. In Zn-rich Cu₂(Zn_1−xMn_x)SnSe₄ mixed crystals, the order parameter Q ∼ 0.7 and drops to Q ∼ 0 (complete Cu/B^II disorder) in the compositional region 0.3 ≥ x ≥ 0.7. In Mn-rich Cu₂(Zn_1−xMn_x)SnSe₄ mixed crystals, adopting the stannite type structure, the order parameter reaches almost Q ∼ 1 (order). Thus, it can be concluded that only Mn-rich Cu₂(Zn_1−xMn_x)SnSe₄ mixed crystals do not show Cu/B^II disorder. A similar trend of the dependence on the chemical composition of both Cu/B^II-disorder and the band gap energy E_g in Cu₂(Zn_1−xMn_x)SnSe₄ mixed crystals was observed.