The cause of the split of 4A4E(4G) Mn2+ excited level measured on minerals spectra is discussed. It is our view that ∆E = |4E(4G) − 4A(4G)| should be considered an important spectroscopic parameter. Among the possible reasons for the energy levels splitting taken under consideration, such as the covalent bond theory, the geometric deformation of the coordination polyhedron and the lattice site’s symmetry, the first one was found to be inappropriate. Two studied willemite samples showed that the impurities occur in one of the two available lattice sites differently in both crystals. Moreover, it was revealed that the calculated crystal field Dq parameter can indicate which of the two non-equivalent lattice sites positions in the willemite crystal structure was occupied by Mn2+. The above conclusions were confirmed by X-ray structure measurements. Significant differences were also noted in the Raman spectra of these willemites.