A novel gram-negative, aerobic, non-spore-forming, rod-shaped, and non-nitrogen-fixing bacterium, named SPY-1(T), was isolated from biological soil crusts collected at Mu Us Sandy Land, China. Based on 16S rRNA sequence similarity, strain SPY-1(T) was most closely related to Neorhizobium alkalisoli CCTCC AB 2014138(T) (98.7%), Neorhizobium huautlense CGMCC 1.2538(T) (98.6%), Neorhizobium galegae DSM 11542(T) (98.4%), Rhizobium wenxiniae 166(T) (97.9%), and Rhizobium smilacinae CCTCC AB 2013016(T) (97.5%). Phylogenetic analysis based on 16S rRNA sequencing and multilocus sequence analysis of partial sequences of atpD-glnII-glnA-recA-ropD-thrC housekeeping genes both indicated that strain SPY-1(T) was a member of the genus Rhizobium. The draft genome of strain SPY-1(T) was 4.75 Mb in size, and the G + C content was 60.0%. The average nucleotide identity (ANI) values to N. alkalisoli CCTCC AB 2014138(T) and R. smilacinae CCTCC AB 2013016(T) were both 84.0%. The digital DNA-DNA hybridization (dDDH) values to N. alkalisoli CCTCC AB 2014138(T) and R. smilacinae CCTCC AB 2013016(T) were 20.9% and 20.2%, respectively. The major cellular fatty acids were summed feature 8 (C-18:1 omega 7c and/or C-18:1 omega 6c) and C-16:0. Based on the data from chemotaxonomic, phylogenetic, and phenotypic evidence, strain SPY-1(T) represents a novel species in the genus Rhizobium, for which the name Rhizobium deserti sp. nov. is proposed. The type strain is SPY-1(T) (= ACCC 61627(T) = JCM 33732(T)).