Overall 175 Brassica napus ecotypes were sown at two locations Yangling (YL) and Kaifang (KF) in China. The root and rhizosphere samples were harvested at the flowering stage at both locations. We performed RNA sequencing for root samples and 16S amplicon sequencing for the rhizosphere samples. Integration of transcriptome and microbiome data will allow us to understand the host gene regulatory of microbiome diversity and composition in Brassica napus.