Abstract: Objective: To study the hybridization efficiency of two fluorescence labeling methods by oligo microarray hybridization. Method: Gene fragments of NS1,NS2a,NS2,NS4a and NS4b were ligated with pMD18-T vector by A/T clone. Then they were labeled by traditional PCR and asymmetric PCR. The labeled samples were examined by the oligo microarray, followed by washing and scanning under the same conditions.Results: Comparing to the traditional PCR labeling method, the asymmetric PCR labeling method showed superior results with enhanced hybridization efficiency. Conclusion: The hybridization efficiency can be enhanced by asymmetric PCR labeling method, which improving the applicability of oligo microarray technology.