In the past four years, outbreaks of acute respiratory diseases associated with canine influenza H3N2 viruses in dogs and cats have been reported in South Korea and China. For prevention of disease from spread of the disease and for administration of timely medical treatments, including countermeasures for quarantine, use of a rapid and highly sensitive detection method are important to detection of the causative viruses. This study was conducted in order to develop a real time RT-PCR for the H3N2 subtype. It was based on primers targeting the highly homologous sequences of matrix, hemagglutinin, and neuraminidase genes. The detection limit of real time RT-PCR was 10 copies/ul with matrix and hemagglutinin genes, and 1 copy with neuraminidase genes, respectively. This real time RT-PCR was as sensitive as virus isolation in 52 clinical samples. The detection system developed in this study might provide more rapid and highly sensitive results than commercial rapid kits based on immunochromatographic assay.