Through organized surfactant templating, mesoporous silica (MPS) was prepared on two different types of substrates with a hydrophilic or hydrophobic surface. In this study, a Si substrate covered with photochemically-grown surface oxide was served as the hydrophilic surface. The hydrophobic surfaces were prepared by forming an organosilane self-assembled monolayer (SAM) on Si substrates through chemical vapor deposition. Octadecyltrimetoxysilane or (heptadecafluoro-1,1,2,2-tetrahydro-decyl) trimethoxysilane was used as a precursor. The morphologies of the deposited MPS on these surfaces were found to be quite different. The MPS formed on the hydrophilic Si substrate consisted of small disk-like features of 2∼5 μm in diameter, while those on the hydrophobic SAM surfaces were continuous thin films. These morphological differences of the deposited MPS were ascribable to the differences in the supramolecular template structure formed on each of the surfaces. Furthermore, in order to study microstructure effects on the MPS growth, a micropatterned SAM/Si, on which hydrophobic regions were spaced alternately with hydrophilic regions at a 5 μm-wide interval, was employed as a sample substrate. On this substrate, MPS was preferentially grown on the hydrophobic regions while the hydrophilic regions remained almost undeposited. The spatial control of surfactant-assembling using the micropatterned SAM surface was successfully accomplished.