The self-assembly of ionically end-capped, symmetric polystyrene-polyisoprene diblock copolymers (PS-b-PI) has been studied. Structural data obtained from small-angle X-ray scattering (SAXS) and transmission electron microscopy (TEM) were correlated with the aggregation behavior of charged chain ends as evidenced by a spin probe using electron paramagnetic resonance (EPR) spectroscopy. The resulting mesomorphic structures were shown to be determined by the chain end topology, i.e., the site where the ionic chain end has been introduced chemically : For omega-functionalized diblock copolymers (monofunctional species) microphase separation is significantly stabilized due to the presence of ionic aggregates within the respective phase separated homopolymer domains. In contrast, for salt-free alpha,omega-macrozwitterionic diblock copolymers a marked perturbation of the block copolymer superstructure was found. In this case, the formation of a network of mixed ionic aggregates creates an additional microdomain interface by joining the chemically distinct blocks at their chain ends. The alteration of the degree of microphase separation as observed for the different functionalities can be attributed to conformational changes of the copolymer chain. Chain end association in the present system is reminiscent of certain covalently joined star and graft copolymers.