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In the crystal structure of the title compound, [Mn(C3H4N2)6][Mn(C3H4N2)3(H2O)3](C12H6O4)2, there are uncoordinated naphthalenedicarboxylate dianions and two kinds of MnII complex cations, both assuming a distorted octahedral geometry. One MnII cation is located on an inversion center and is coordinated by six imidazole molecules, while the other MnII cation is located on a twofold rotation axis and is coordinated by three water molecules and three imidazole units. The naphthalenedicarboxylate dianions are linked to both MnII complex cations via O—H...O and N—H...O hydrogen bonding, but no π–π stacking is observed between aromatic rings in the crystal structure.