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Background Paenibacillus polymyxa WLY78 is a Gram-positive, endospore-forming and N 2 -fixing bacterium. Our previous study has demonstrated that GlnR acts as both an activator and a repressor to regulate the transcription of the nif ( ni trogen f ixation) operon ( nifBHDKENXhesAnifV ) according to nitrogen availability, which is achieved by binding to the two GlnR-binding sites located in the nif promoter region. However, further study on the GlnR-mediated global regulation in this bacterium is still needed. Results In this study, global identification of the genes directly under GlnR control is determined by using chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) and electrophoretic mobility shift assays (EMSA). Our results reveal that GlnR directly regulates the transcription of 17 genes/operons, including a nif operon, 14 nitrogen metabolism genes/operons ( glnRA , amtBglnK , glnA1 , glnK1 , glnQHMP , nasA , nasD1 , nasD2EF , gcvH , ansZ , pucR , oppABC , appABCDF and dppABC) and 2 carbon metabolism genes ( ldh3 and maeA1 ). Except for the glnRA and nif operon, the other 15 genes/operons are newly identified targets of GlnR. Furthermore, genome-wide transcription analyses reveal that GlnR not only directly regulates the expression of these 17 genes/operons, but also indirectly controls the expression of some other genes/operons involved in nitrogen fixation and the metabolisms of nitrogen and carbon. Conclusion This study provides a GlnR-mediated regulation network of nitrogen fixation and the metabolisms of nitrogen and carbon.