【Objective】The present experiment was conducted to study the expression of relative drought-resistant gene in drought-resistant hybrid offspring（K0959） of Brassica napus and Brassica juncea. 【Method】 cDNA-AFLP technique was used to analyze the differential gene expression in leaves of drought-resistant K0959 under 25% (w/v) PEG-6000 stress and control condition. 【Result】Amongst 128 primer combinations， 16 were screened to get 30 differential fragments in PCR amplification. After re-amplification， 15 differential fragments， ranging from 102-384 bp in size， were obtained. Among 15 differential fragments， 7 fragments including 4 non-repetitive TDFs （2B， 2D， 3-2B and 14B） showed high homology with mRNA of Arabidopsis； one with Brassica oleracea （3D） and one with Brassica napus （2C）， while 6 fragments （D2-1，6A and 9-2C，etc） ranging from 102-240 bp did not showed homology with known genes and their sequences were submitted in GenBank as new genes. The 6 TDFs were found to take part in energy metabolism， cellular transportation pathways， cell cycle and DNA processing， etc. 【Conclusion】 The obtained differentially expressed genes will help in elucidating the gene regulatory mechanism of drought-resistance in hybrids of B. napus and B. juncea.