We have examined the electronic and molecular structure of 3,7-diaminophenothiazin-5-ium dye (thionine) in the electronic ground state and in the lowest excited states. The electronic structure was calculated using a combination of density functional theory and multi-reference configuration interaction (DFT/MRCI). Equilibrium geometries were optimized employing (time-dependent) density functional theory (B3LYP functional) combined with the TZVP basis set. Solvent effects were estimated using the COSMO model and micro-hydration with up to five explicit water molecules. Our calculated electronic energies are in good agreement with experimental data. We find the lowest excited singlet and triplet states at the ground state geometry to be of p→p* (S1, S2, T1, T2) and n→p* (S3, T3) character. This order changes when the molecular structure in the electronically excited states is relaxed. Geometry relaxation has almost no effect on the energy of the S1 and T1 states (~0.02 eV). The relaxation effects on the energies of S2 and T2 are moderate (0.14–0.20 eV). The very small emission energy results in a very low fluorescence rate.While we were not able to locate the energetic minimum of the S3 state, we found a non-planar minimum for the T3 state with an energy which is very close to the energy of the S1 minimum in the gas phase (0.04 eV above). When hydration effects are taken into account, the n→p* states S3 and T3 are strongly blueshifted (0.33 and 0.46 eV), while the p→p* states are only slightly affected (<0.06 eV).