We report a self-recognition phenomenon based on an assembly process in a homogeneous dilute aqueous solution of two nano-scaled, spherical polyprotic metal oxide-based macroions (neutral species in crystals), also called Keplerates of the type [(linker)(30)(pentagon)(12)]=[{M(H2O)}(30){(Mo)Mo-5}(12)] where M is Fe-III or Cr-III. Upon deprotonation of the neutral species, the resulting macroions assemble into hollow "blackberry"-type structures through very slow homogeneous dimer-oligomerization processes. Although the geometrical surface structures of the two macroions are practically identical, mixtures of these form homogeneous superstructures, rather than mixed species. The phase separation is based on the difference in macroionic charge densities present during the slow homogeneous dimer or oligomer formation. The surface water ligands' residence times of Cr-III and Fe-III differ markedly and lead to very different interfacial water mobilities between the Keplerates.