Molecular-level insight into the frictional properties of fluorinated self-assembled monolayers (SAMs) was achieved by combining two recently developed techniques that operate at the subnanometer scale: control of the interfacial composition through molecular self-assembly and tribological measurements performed with the atomic force microscope. To explore the origin of frictional forces in fluorinated films, the frictional properties of two classes of alkanethiols adsorbed on single crystal gold were measured and compared. In these studies, films of equivalent chain length, packing density and packing energy, but different termination (methyl vs trifluoromethyl), were characterized and investigated. For these films, in which the only detectable difference was the outermost chemical structure composition, a factor of 3 increase in the frictional response was observed in going from the hydrogenated to the fluorinated film. These results support the conclusion that chemical structure/composition alone plays an integral role in determining the frictional properties of an interface. We propose that the difference in friction arises predominantly from the difference in size of the methyl and trifluoromethyl groups.