The molecular assembly of p-iodo-phenyl octadecyl ether (I-POE), p-iodo-phenyl docosyl ether (I-PDE) and a binary mixture of these two molecules on graphite has been studied using a scanning tunneling microscope. Each molecular system self-assembles on the graphite surface to form a stable monolayer. For the binary system, the I-POE and I-PDE molecules do not mix on the surface, preferring instead to form isolated monolayer domains. Here, the I-POE molecules are preferentially adsorbed on the graphite surface, due to the effects of alkyl chain length and the functional group on the monolayer structure.