A novel 1-aminocyclopropane-1-carboxylate deaminase producing bacterium, Gram- stain-negative, aerobic, motile, rod-shaped strain designated YM1C-6-2^T was isolated from rhizosphere of maize grown in Northeast China. The 16S rRNA gene sequence analysis indicated that strain YM1C-6-2^T belongs to the genus Mesorhizobium and is closely related to Mesorhizobium alhagi CCNWXJ12-2^T and M. camelthorni CCNWXJ40-4^T with sequence similarities of 98.4% and 97.9%, respectively. Multilocus sequence analysis of other housekeeping genes revealed that the new isolates YM1C-6-2^T forms a phylogenetically group with some species in the genus Mesorhizobium. The genome size of strain YM1C-6-2^T was 5.51 Mb, comprising 5378 predicted genes with a DNA G+C content of 64.5%. The average nucleotide identity and digital DNA–DNA hybridization comparisons between YM1C-6-2^T and the most related type strains showed values below the accepted threshold for species discrimination. The major fatty acids of strain YM1C-6-2^T were C_19:0 cyclo ω8c (47.5%), summed feature 8 (C_18:1ω7c and/or C_18:1ω6c) (19.5%) and C_16:0 (15.1%), which differed from the closely related reference strains in their relative abundance. The major polar lipids consist of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and an unidentified aminophospholipid. The predominant ubiquinone was identified as Quinone 10. Phenotypic and biochemical analysis results indicated that strain YM1C-6-2^T can be distinguished from closely related type strains. Based on the above results, strain YM1C-6-2^T represents a novel species of the genus Mesorhizobium, for which the name Mesorhizobium rhizophilum sp. nov. is proposed with YM1C-6-2^T (= CGMCC 1.15487^T = DSM 101712^T) as the type strain.