To understand epitaxial growth of organic molecules from a phenyloctane solution, mono-molecular layers of a non-planar isoindoline derivative formed on the graphite (0001) surface were investigated by STM. The observed images showed that the layer is composed of many small single-crystalline 2D domains, where the lattice orientation was analyzed with respect to the graphite surface lattice. As a result, the molecules adsorbed with its isoindoline frame to be parallel to the HOPG surface and the epitaxial orientations were slightly fluctuated around commensurate orientation from domain to domain. This is named pseudo-commensurate epitaxy, which is resulted from a size effect; that is, due to broadening of Laue functions appearing in an expression of lattice-lattice interaction energy at interface of deposited layer and substrate surface.