Background Production of rapeseed(Brassica napus.L),one of the most important oil crops,is affected by waterlogging.However,genetic basis of waterlogging tolerance is largely unknown in rapeseed.It is important to study molecular mechanism of waterlogging tolerance in rapeseed.Methods The transcriptome under 0h and 12h of waterlogging was assayed in roots of seedlings for ZS9,a tolerant rapeseed variety,using digital gene expression(DGE).Key Results 4432 differentially expressed genes were identified,containing 1709 up-regulated and 2723 down-regulated ones.Both of GO(Gene Ontology)analysis of all annotated genes and the top 200 highly expressed genes revealed some pathways related with “oxidation reduction”,“secondary metabolism”,“transcription regulation”,and “translation regulation”,“universal stress” were enhanced under waterlogging.Genes related with “transcription regulation” were up to 18.6%of induced ones,and some genes related with “DNA/RNA binding” and “translation regulation” were also induced by waterlogging.96 genes related with protein degradation were down-regulated by the stress,accounting for up to 6.3%of reduced genes.Conclusions Under waterlogging,expression of genes is mediated by regulation at multiple levels,including regulation of transcription,post-transcription,translation,and post-translation.At translation level,it may regulate synthesis efficiency of different genes through manipulating the abundance of different translation machineries.Additionally,down-regulation of some of genes responsible for protein degradation might play a negative role for waterlogging tolerance.Those genes involved in these pathways should be studied further.