Two rod-shaped macroanions, ((C4H9)4N)7[Mo6O18NC(OCH2)3XMo6O18(OCH2)3CNMo6O18] (X = Mn(III) (1), Fe(III) (2)), with almost identical charge densities and morphologies except for their different encapsulated central metal atoms were each observed to self-assemble into "blackberry"-type supramolecular structures in their dilute solution, driven by the counterion-mediated attraction. Amazingly, the two macroions remained self-sorted and self-assembled into homogeneous assemblies in their mixed solutions, demonstrating a self-recognition behavior between two highly similar macroions during their assembly process, as confirmed by DLS, SLS, and TEM/EDS analysis. This self-recognition behavior can be explained by the slightly different charge distributions of the macroanions resulting from their different central atoms (confirmed by theoretical DFT calculations and dissociation experiments) and the high activation energy of the slow assembly process, which suppresses the formation of hybrid oligomers at the beginning of the self-assembly process. This work confirms that the long-range counterion-mediated electrostatic attraction is sensitive to the small difference in macroions and consequently offers the possibility for delicate selectivity and preference among different macroions. This phenomenon might be directly related to (and be the important reason for) some recognition behaviors in biological systems.