Divalent cations, particularly magnesium, play an important role in the stabilization of nucleic acids and in their biochemistry. Of special interest is the strong affinity of a hydrated magnesium ion for guanine. To investigate the nature of this interaction, we calculated the interaction energy (IE) for eight optimized complexes in which tetra-, penta-, and hexahydrated magnesium ions were initially placed in the plane of guanine near the O6 and N7 binding sites. Results at the RHF/6-311G**//RHF/6-311++G** level indicate that the guanine-tetrahydrated magnesium ion complex has the highest value of the IE. However, the formation of the tetrahydrated magnesium ion from a hexahydrated ion decreases the energy of this complex and, overall, the hexahydrated ion is considered to be more stable. We also investigated the binding site of a hexahydrated magnesium ion located in a high-resolution crystal structure of the dodecamer [d(CGCGAATTCGCG)](2). Complexes of the hexahydrated magnesium ion with the individual and combined G2 and G22 bases extracted from the crystal structure were also considered and Natural Energy Decomposition Analysis used to partition the IEs. The results show that water-mediated charge transfer from guanine to magnesium plays an important role in the stabilization of these guanine-water-magnesium complexes and occurs by a cooperative mechanism.