Abstract: In order to determine the viral species and strains of the Brassica juncea var. gemmifera Lee et Lin（B. jg）and Brassica juncea var. tumida Tsen et Lee（B. jt）virus disease in Chongqing，RT-PCR and sequences analysis were used to detect and identify virus species and strains in the samples collected from 18 towns of 13 counties in Chongqing area. The results showed that in the 57 B. jg samples，31.58%，85.86%，49.12%，59.65% and 77.19% were infected by Cucumber mosaic virus（CMV），Turnip mosaic virus（TuMV），Tobacco mosaic virus（TMV），Potato virus X（PVX）and Brassica yellows virus（BrYV），respectively. Among the virus infected B. jg samples，87.72% were mix-infected by more than two viral species，and 45.61% samples were mix-infected by three viral species. While，in the 41 B. jt samples，36.59%，73.17%，75.61% and 70.73% were infected by CMV，TuMV，PVX and BrYV，respectively. Among the virus infected B.jt samples，80.49% were mix-infected by more than two viral species，and 51.22% were mix-infected by three viral species. Based on the amplification，sequencing，and phylogenetic analysis of the CP gene of each virus，TuMV in B. jg and B. jt was clustered into the World-B group，CMV was clustered into subgroup Ⅰ，and PVX was identified to be the X3 strain. Although BrYV and TMV had high sequence homology in CP gene with each of their previously reported strains，there was correlation between the isolates and geographic regions. Furthermore，this is the first report of the occurrence of BrYV in Chongqing.

Key words: Brassica juncea var. gemmifera Lee et Lin, Brassica juncea var. tumida Tsen et Lee；virus disease；RT-PCR, detection, identification, Capsicum spp., genetics, breeding