The nucleation and growth of pentacene thin films are controlled largely by the energies associated with the interfaces. We have used low-energy electron microscopy (LEEM) and photoemission electron microscopy (PEEM) to investigate the nucleation and growth of pentacene thin films on Si(001) surfaces modified with two different molecular monolayers. Clean Si(001)-(2 × 1) surfaces were modified with either 1,5-cyclooctadiene or 1-dodecene prior to pentacene growth to study the effects of exposed π bonds at the interface, orientation of those π bonds relative to each other, and rigidity of the molecular layer on pentacene nucleation, growth, and crystalline orientation. Both molecular monolayers weaken the substrate-pentacene interaction sufficiently to allow for low pentacene nucleation density and good pentacene diffusion, leading to the growth of pentacene grains as large as 100 µm. Pentacene grows epitaxially on both functionalized surfaces, adopting an orthorhombic unit cell that follows the orientation of the underlying Si surface reconstruction. Our results show that in addition to improving the ultimate size of pentacene crystals, molecular monolayers are able to impose the substrate orientation on pentacene nuclei and thereby control the crystalline orientation of the thin film.