We report a new type of molecular sensor using a Au nanowire (NW)-Au nanoparticles (NPs) conjugated system. The Au NW-NPs structure is fabricated by the self-assembly of biotinylated Au NPs on a biotinylated Au NW through avidin; this creates hot spots between NW and NPs that strongly enhance the Raman signal. The number of the Au NPs attached to the NW is reproducibly proportional to the concentration of the avidin, and is also proportional to the measured surface-enhanced Raman scattering (SERS) signals. Since this well-defined NW-NPs conjugated sensor is only a few micrometer long, we expect that development of multiplex nanobiosensor of a few tens micrometer size would become feasible by combining individually modified multiple Au NWs together on one substrate.