A method for rapid detection of the highly virulent Porcine Reproductive and Respiratory syndrome virus (H-PRRSV) was developed using fluorescence quantitative PCR assay (FQ-PCR). The Taqman probe and a pair of specific primers and were designed based on Nsp2 gene with 87-base-pairs sequence deletion. Then the FQ-PCR method was developed by optimization of the reaction conditions, which showed high specificity and sensitivity, and well differentiated H-PRRSV form other viruses. 1TCID50/ml of the H-PRRSV could be detected by this method. Besides, similar positive percentages of 38 tissue specimens (60.5%) were found using FQ-PCR assay or conventional PCR assay.