Soil waterlogging is a serious constraint to crop production. We investigated the physiological responses of rape (Brassica napus L.) seedlings to waterlogging stress and analyzed global gene transcription responses in the aerial leaves of waterlogged rape seedlings. Seedlings of 'Tammi' and 'Youngsan' cultivars were subjected to waterlogging for 3 and 6 days and recovery for 5 days. Waterlogging stress caused a significant decrease in leaf chlorophyll content and premature senescence of the leaves. Maximal quantum efficiency of PSII (F(v)/F(m)) decreased in the waterlogged seedlings compared with the control plants. To evaluate whether the observed physiological changes in the leaves are associated with the differential regulation of gene expression in response to waterlogging stress, we analyzed the global transcriptional profile of leaves of 'Tammi' seedlings that were exposed to waterlogging for a short period (36 and 72 h). SolexaQA RNA-seq analysis revealed that a total of 4,484 contigs (8.5 %) of all contigs assayed (52,747) showed a twofold change in expression after 36 h of the start of waterlogging and 9,659 contigs (18.3 %) showed a twofold change after 72 h. Major genes involved in leaf photosynthesis, including light reactions and carbon-fixing reactions, were downregulated, while a number of genes involved in the scavenging of reactive oxygen species, degradation (proteins, starch, and lipids), premature senescence, and abiotic stress tolerance were upregulated. Transcriptome analysis data suggested that the aerial leaves of waterlogged rape seedlings respond to hypoxia by regulating the expression of diverse genes in the leaves.