Abstract:Southern bean mosaic virus (SBMV) is in the A2 list concerned to China. The coding region of cp gene from Japan isolate of SBMV was sequenced. It comprised 801 nucleotides and encoded a putative protein of 266 amino acids. The nucleotide and amino acid sequence of cp gene of this isolate shared 83% to 97% and 86% to 97% similarities to those of other SBMV isolates or strains, respectively. A pair of primers and a TaqMan-MGB probe based on the conserved nucleotide sequence of coat protein (CP) gene of SBMV isolates were designed and synthesized. A novel one step assay of real-time fluorescent RT-PCR was established to detect SBMV. The limit content of the detection was 0.16pg and the optimal content was 0.16ng.