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The transition of a plant from vegetative to reproductive stage is controlled by a large group of genes, which respond to environmental and endogenous stimuli. Application of methyl jasmonate (MeJA) and gibberellins (GA3) to oilseed plants (Brassica napusL.) interrupts the delicate endogenous balance and results in various floral organ abnormalities. Exogenous MeJA or GA3influences the transcriptome at the initial flowering stage in Arabidopsis,but the corresponding changes of transcriptome in floral tissues of oilseed rape remain unknown. In this study, cDNA-amplified fragment length polymorphism (cDNA-AFLP) was analyzed to identify genes whose expression was modulated by application of MeJA and GA3to flower buds. A total of 2 787 cDNA fragments were counted using 64 primer pair combinations, and bands larger than 50 bp were compared among four treatments, namely, water control, MeJA (50 μmol L−1), MeJA (100 μmol L−1), and GA3(50 μmol L−1). Overall, 168 transcript-derived fragments (TDFs) were differentially expressed among the treatments. The expression pattern of some TDFs was confirmed by semi-quantitative RT-PCR analysis, and a group of 106 differentially displayed TDFs was cloned and sequenced. Homologs of Arabidopsisgenes were identified and classified into 12 functional categories. A total of 34, 39, and 24 TDFs were responsive to GA3, MeJA, and both GA3and MeJA, respectively. This finding indicated that cross-talk between these two hormones may be involved in regulating flower development. This study provides potential target genes for manipulation in terms of flowering time and floral organ initiation, important agronomic traits of oilseed rape.