The coordination behavior of two Schiff base ligands, N,N'-bis(3-carboxysalicylidene)ethylenediamine (H2L1) and N,N'-bis(3-carboxysalicylidene) propylenediamine (H2L2), towards magnesium ions is reported. The ligands show different binding site selectivity for Mg2+ depending on the solvent. In complexes isolated from aqueous or methanolic solutions the metal ion resides in the outer O2O2 compartment. The X-ray analysis of the complex of H2L1 showed the complex to be dimeric with magnesium being coordinated by two phenolate and two carboxylate oxygens, a bridging phenolate oxygen, and a water ligand. In aprotic solvents like dimethylsulfoxide (DMSO) and dimethylformamide (DMF) magnesium migrates to the inner N2O2 binding site. In DMSO solution containing small amounts of water, both isomers co-exist. A similar solvent-dependent site selectivity is not observed for zinc ions.