The performance of organic semiconductor devices is strongly affected by the interface energetics at the junctions between the constituent materials. A large group of organic semiconductors consists of rodlike small molecules that crystallize upon deposition with a molecular orientation dependent on the specifics of the molecule–molecule and molecule–substrate interactions. By means of Kelvin probe force microscopy (KPFM), this work studies naphthyl end-capped oligothiophene, 5,50-bis(naphth-2-yl)-2,20-bithiophene (NaT2), deposited on samples of pristine SiO 2 and samples of graphene-covered SiO 2. The crystal molecular orientation of NaT2 is dependent on the substrate on which it is deposited. On SiO 2, the NaT2 molecules are predominately upright standing, forming crystallites with distinct terrace heights of 2.0±0.1nm. Measurements indicate formation of an initial wetting layer in the NaT2-SiO 2 system for the upright standing molecules. When deposited on graphene, the molecules additionally form fibrous structures with heights of 10−115nm consisting of molecules lying down (face-on orientation). Using KPFM, a difference in the local contact potential difference (CPD) of upright standing NaT2 and face-on oriented structures on graphene is measured to be −0.16±0.04V, indicating a work function difference between the two system configurations, which is confirmed through Density Functional Theory calculations.