Thermotropic polyglutamates with photochromic azobenzene side groups are polymers of the "hairy rod" type. They form LB multilayer assemblies, in which the rod-like macromolecules are oriented in the dipping direction. The initial LB films have a well-defined bilayer structure in which the rod-like azobenzene moieties are tilted toward the a-helical backbones and form R-aggregates. The change of aggregation and orientational order of the azobenzene chromophores is studied for polyglutamates with different spacer lengths upon irradiation and annealing. The lamellar order and in-plane anisotropy of the chromophores is irreversibly lost on UV irradiation. New ordered structures with a more symmetric distribution of the side chains around the main chain helix, a modified spacing, changed aggregation, and a different in-plane anisotropy are established after subsequent vis irradiation or annealing. The established supramolecular order strongly depends on the spacer length. A shorter spacer (C-2) between the backbone and the photochromic moiety causes an isotropic in-plane distribution of the chromophores, whereas in the case of longer spacers (C-4 or C-6) an arrangement of the chromophores parallel to the main chain helices is restored. The change in the molecular arrangement of the side groups is controlled by the ordering tendencies and the dynamic properties of the combined liquid crystalline main and side chain polymers.