An azobenzene-terminated long chain alkanethiol was used for self-assembly onto gold substrates. A remarkable lack of activity for trans-to-cis photoisomerization; in the film was evaluated quantitatively using a combined photochemical-electrochemical method. The film structure was then examined in detail by means of UV-visible spectroscopy and atomic force microscopy (AFM). The results indicated that the azobenzene-containing molecules were extraordinarily densely packed in the SAM. A pinwheel structure, in which the long axes of the azobenzene moieties are parallel to each other and the neighboring short axes are mutually perpendicular to each other, was supported by UV-visible and IR evidence and was observed directly with AFM. This structure is consistent with the dense packing. By comparing with the structure of the same molecule in the crystalline state, it was found that the pinwheel structure can be ascribed to a combination of the covalent bonding between the sulfur head-groups of the molecule and Au atoms of the substrate, the strong van der Waals interaction of the alkane chains, and interactions between neighboring azobenzene moieties.