The effect of chemical heterogeneity on the adsorption of Methyl Orange (MO) in aqueous solutions was investigated by atomic force microscopy (AFM). On hydrophilic mica, a small number of disordered islands of Methyl Orange were formed. However, after deposition of self-assembled monolayers (SAMs) of octadecyltrichlorosilane (OTS) on mica, MO molecules adsorbed extensively and selectively on the hydrophobic OTS SAMs. Most importantly, the MO molecules on hydrophobic domains were highly ordered and almost perpendicular to the OTS surface.