To explore the effect of the substrate surface potential relief on the self-assembly of the adsorbed organic molecules, adsorption of tryptanthrin molecules on the various reconstructed Si(111) surfaces has been studied using scanning tunneling microscopy. The set of the Si(111) surface reconstructions under consideration includes atomically clean adsorbate-free Si(111)7 × 7 and metal-induced Si(111)4 × 1-In, Si(111)’5.5 × 5.5’-Cu, and Si(111)√3 × √3-Ag surfaces, each having specific surface potential relief. It has been found that on the Si(111)7 × 7 surface, which is characterized by a high density of dangling bonds, the tryptanthrin molecules are randomly trapped by dangling-bond Si adatoms without forming any ordered array. On the quasi-one-dimensional Si(111)4 × 1-In surface, the tryptanthrin molecules are self-assembled into the meandering molecular chains aligned along the In-atom rows of the 4 × 1-In reconstruction. On the Si(111)’5.5 × 5.5’-Cu surface, having a honeycomb-like potential relief associated with its discommensurate structure, the tryptanthrin molecules form an array of the supramolecular complexes displaying a ring-shaped STM appearance and containing presumably two molecules each. On the atomically smooth and inert Si(111)√3 × √3-Ag surface with very shallow potential relief, the adsorbed tryptanthrin forms at room temperature a two-dimensional gas of highly mobile molecules, which condensates into random disordered molecular islands upon cooling sample to 110 K.