The reaction in water of the N-benzyliminodiacetate−copper(II) chelate ([Cu(NBzIDA)]) and the adenine:thymine base pair complex (AdeH:ThyH) with a Cu/NBzIDA/AdeH/ThyH molar ratio of 2:2:1:1 yields [Cu₂(NBzIDA)₂(H₂O)₂(μ-N7,N9-Ade(N3)H)]·3H₂O and free ThyH. The compound has been studied by thermal, spectral, and X-ray diffraction methods. In the asymmetric dinuclear complex units both Cu(II) atoms exhibit a square pyramidal coordination, where the four closest donors are supplied by NBzIDA in a mer-tridentate conformation and the N7 or N9 donors of AdeH, which is protonated at N3. The μ-N7,N9 bridge represents a new coordination mode for nonsubstituted AdeH, except for some adeninate(1−)−[methylmercury(II)] derivatives studied earlier. The dinuclear complex is stabilized by the Cu−N7 and Cu−N9 bonds and N6−H(exocyclic)···O(carboxyl) and N3−H(heterocyclic)···O(carboxyl) interligand interactions, respectively. The structure of the new compound differs from that of the mononuclear compound [Cu(NBzIDA)(Ade(N9)H)(H₂O)]·H₂O, in which the unusual Cu−N3(AdeH) bond is stabilized by a N9−H···O(carboxyl) interligand interaction and where alternating benzyl-AdeH intermolecular π,π-stacking interactions produce infinite stacked chains. The possibility for ThyH to be involved in the molecular recognition between [Cu(NBzIDA)] and the AdeH:ThyH base pair is proposed.