Pulsed-force-mode atomic force microscopy (PFM-AFM), with functionalized probe tips, was applied to discrimination of chemical functionalities of a binary system of mixed self-assembled monolayers (SAMs) consisting of CH3- and COOH-terminating alkane thiols. PFM-AFM enabled simultaneous imaging surface topography and distribution of adhesive forces between the tip and sample surfaces. Since the adhesive forces were directly related to interaction between the chemical functional groups on the tip and sample surfaces, we combined the adhesive force mapping by PFM-AFM with the chemically modified tips to accomplish imaging the sample surface with the chemical sensitivity. The adhesive force mapping by PFM-AFM with the CH3-modified tips in pure water clearly discriminated the hydrophobic CH3-terminating domains embedded in the COOH-terminating SAM matrix.