A novel method for identifying DNA microarrays based on ZnO/Au nanocomposites functionalized with thiol-oligonucleotide as probes is descried here. DNA labeled with ZnO/Au nanocomposites has a strong Raman signal even without silver acting as a surface-enhanced Raman scattering promoter. X-ray photoelectron spectra confirmed the formation of a three-component sandwich assay, i.e., constituted DNA and ZnO/Au nanocomposites. The resonance multiple-phonon Raman signal of the ZnO/Au nanocomposites as a spectroscopic fingerprint is used to detect a target sequence of oligonucleotide. This method exhibits extraordinary sensitivity and the detection limit is at least 1 fM.