In an attempt to study the reaction of multifunctional organic molecules with a Si surface, we examined the adsorption of phenylacetylene (HCequivalent toC-C6H5) and 1-phenyl-1-propyne (H3C-Cequivalent toC-C6H5) on Si(100)-(2 x 1) by using scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. The extra methyl group in 1-phenyl-1-propyne was used as a marker for determining the molecular orientation in the STM image. Two distinct adsorption structures were revealed for these molecules. One is analogous to the so-called di-sigma adsorption structure of acetylene, involving the binding of a Cequivalent toC group of molecules on top of a Si dimer. In the other structure, which is unique, a molecule adsorbs across the valley between two Si dimer rows (the "valley-bridge" structure) such that a phenyl ring binds to two Si atoms in one dimer row and a Cequivalent toC group binds to the next dimer row. DFT calculations predicted the adsorption energy of phenylacetylene to be 2.44-2.67 eV in the di-sigma structure and 0.45-1.59 eV in the valley-bridge structures.