Objective To study the double restriction fluorescent labeling (DRFL) method for fluorescent labeling of trace DNA samples and its effect in enhancing the pathogen detection sensitivity of microarray assays. Method SARS-CoV RNA samples were reversely transcribed and then further amplified with the restriction display (RD)-PCR and fluorescently labeled by conventional restriction labeling directly with Cy-universal primer and the novel double labeling with Cy-universal primer and Cy-dNTP. The labeled samples were applied to the microarray with the viral probes, processed and analyzed. Results Compared with the conventional method, DRFL labeling resulted in 3.5835 times higher fluorescent intensity of all the SARS probes on average, even though increased fluorescent intensities for different probes varied considerably. Conclusion Signal to noise ratio can be enhanced by the DRFL method which improves the sensitivity of microarray technology in trace pathogen detections.