The self-organizing structures formed by a water-soluble perylene diimide dye (PDI) have been studied by several experimental techniques as potential templates for the preparation of hybrid nanomaterials. The dye forms chromonic-nematic and hexagonal liquid crystals in water. The aggregates in liquid crystals consist of one-molecule-wide stacks. From the changes in the solution proton NMR chemical shifts with concentration, it appears that adjacent molecules are twisted. There is significant broadening of the aromatic resonances at higher concentrations, arising from nonmotionally averaged dipole-dipole coupling between adjacent aromatic hydrogens. This is attributed to slow overall rotation of the aggregates in solution, suggesting that they grow up to several tens of nanometers. Dye aggregates serve as templates for the formation of silica tubules (1-5 μm length, average diameter ≈300 nm), with aligned and very thin (1-2 nm) dye nanostripes embedded in the walls. The silica tubes precipitated from solution are formed by the cooperative interaction between PDI and silica species during the sol-gel reaction. Upon calcination, silica nanotubules with supermicroporous walls are obtained. In comparison with conventional surfactant systems, the use of π-π stacked chromonic aggregates brings new possibilities for the templated fabrication of pores with sizes below the mesoporous range. Materials could find applications in photovoltaics as well as in shape selective catalysis and adsorption.