The primers were designed by use of the sequences of chromosome-specific genes in Brassica juncea and B. napus as template and genotyping was performed to trace the transmission of chromosomes in the F2 and BC1F1 populations of B. juncea×B. napus hybrids. The results showed that the chromosomes An03, An08, An09, An10, Cn03 and Cn09 from B. napus and Aj03 and Aj10 from B. juncea were not lost in the BC1F1 population, while loss frequency of the chromosome Bj07 was the highest, 62.83%. In the F2 population, the Aj-and Bj-genome chromosomes from B. juncea were lost more frequently than the An- and Cn- genome from B. napus, and the chromosomes An08 and Cn03from B. napus and Bj08 from B. juncea were lost at frequency of 1.36%, 1.36% and 0.90%, respectively. However, the chromosome Bj07 was lost at 56.56 %. For the BC1F1 progeny, with the mean seed setting of 0.60, up to 5.31 under self-pollination, and 1.95, up to 12.85 under open pollination. For the F2 progeny the mean seed setting of 0.66, up to 17.70 under self-pollination, and 2.18, up to 23.05 under open pollination. These results provided a theoretical basis for breeding by interspecific cross of B. juncea and B. napus, which would help enhance germplasm of B. napus by introducing elite genes of B. juncea.