The role of molecular reorientation processes in the self-assembly of anisotropic molecules, such as pentacene (Pn) is studied utilizing a unique capability of low-energy electron microscopy (LEEM) for the real-time investigation of the film growth. In Pn film on SiO2, a layer-by-layer growth is observed, albeit different from the expected Volmer–Weber growth mode typical for the systems with lower adhesion (weak interfacial interaction). The observed growth mechanism is also different than conventional concept of layer-by-layer, or Frank van der Merwe growth. In the Pn/SiO2 system the nucleation density decreases in each consecutive layer, at least up to four monolayers. This growth mechanism is hereafter named inverse Stranski-Krastanov growth. Furthermore, in this growth system the second layer islands nucleate preferentially at the domain boundaries formed by the interconnections of the bottom (first layer) domains. The top layer overgrows bottom layer with its own, initial in-plane crystal orientation, regardless of the in-plane orientations in underlying Pn domains. The dark-field LEEM imaging allows us to distinguish between Pn domains having different azimuthal direction of molecular tilt. LEEM intensity versus start voltage (LEEM I–V) curves taken in the vicinity of mirror potential from the first and second layer Pn islands show that the surface potential of the second layer is higher by about 0.05 eV than that of the first layer, while the surface potentials for the epitaxial and non-epitaxial parts of the second layer island are identical.