The synthesis of molecular cluster pairs is a challenge for coordination chemists due to the potential applications of these species in molecular spintronics or quantum computing. The ligand H4L, 1,3-bis-(3-oxo-3-(2-hydroxyphenyl)-propionyl)-2-methoxybenzene, has been successfully used to obtain a series of such complexes using the basic Fe(III) trinuclear carboxylates as starting materials. Synthetic control has allowed the isolation of the two molecular cluster pairs that form the composite [Fe4O2(PhCO2)(6)(H2L)(pz)](2)[Fe3O-(PhCO2)(5)(py)(H2L)](2) (1). The dimers of trinuclear units, [Fe3O(PhCO2)(5)(H2O)(H2L)](2) (2) and [Fe3O(o-MePhCO2)(5)(H2L)(py)](2) (3), and the dimers of tetranuclear units, [Fe4O2(PhCO2)(6)(H2L)(pz)](2) (4) and [Fe4O2(o-MePhCO2)(6)(H2L)(pz)](2) (5), are presented here. The magnetic properties of the reported aggregates show that they are pairs of semi-independent clusters weakly interacting magnetically as required for two-qubit quantum gates.