Guanidinium groups present in peptides and dendritic polymers induce their efficient transport through liposomal and cell membranes. Transmembrane crossing of these polymers is affected by their structural features and is critically dependent on the number of guanidinium groups present. Furthermore, the interaction of the guanidinium groups with phosphate groups, both located on liposomal surfaces, triggers a series of processes involving a reorganization of the self-assembled lipids and inducing the formation of multicompartment systems. These observations consistent throughout a diversity of interacting complementary liposomes, support a hypothesis that molecular recognition of liposomes induces the formation of multicompartment structures.