RNA sequencing of the sensitive GH01 variety of Brassica napus L. seedling roots under 12 h of waterlogging was compared with previously published data of the ZS9 tolerant variety to unravel genetic mechanisms of waterlogging tolerance beyond natural variation. A total of 2 977 genes with similar expression patterns and 17 genes with opposite expression patterns were identified in the transcription profiles of ZS9 and GH01. An additional 1 438 genes in ZS9 and 1 861 genes in GH01 showed strain specific regulation. Analysis of the overlapped genes between ZS9 and GH01 revealed that waterlogging tolerance is determined by ability to regulate genes with similar expression patterns. Moreover, differences in both gene expression profiles and abscisic acid(ABA) contents between the two varieties suggest that ABA may play some role in waterlogging tolerance. This study identifies a subset of candidate genes for further functional analysis. RNA sequencing of the sensitive GH01 variety of Brassica napus L. seedling roots under 12 h of waterlogging was compared with previously published data of the ZS9 tolerant variety to unravel genetic mechanisms of waterlogging tolerance beyond natural variation. A total of 2 977 genes with similar expression patterns and 17 genes with the opposite expression patterns were identified in the transcription profiles of ZS9 and GH01. An additional 1 438 genes in ZS9 and 1 861 genes in GH01 showed strain specific regulation. Analysis of the overlapped genes between ZS9 and GH01 revealed that waterlogging tolerance is determined by ability to regulate genes with similar expression patterns. Moreover, differences in both gene expression profiles and abscisic acid (ABA) contents between the two varieties suggest that ABA may play some role in waterlogging tolerance. This study identifies a subset of candidate genes for further functional analysis.