Bacillus amyloliquefaciens FZB42 is a model organism for Gram positive soil bacteria associated with plant roots and beneficial to plant growth.It is of immense importance to understand metabolic mechanisms of this class of bacteria adapting to rhizosphere.In this work employing differential RNA sequencing and Northern blot, we systematically identified mRNAs expressed in response to different growth phases as well as non-coding regulatory RNAs in FZB42.A large suit of TSSs and polycistronic operons were also identified and the genome annotation was improved.The result we obtained provides valuable data for investigation of Bacillus gene expression and molecular details of rhizobacterial interaction with host plants.