The antimony-oxidizing strain Klebsiella aerogenes X was isolated from Sb contaminated soil. A total of 8.00 Mbp of data were obtained, representing about 100-fold coverage of the genome. The draft genome of Klebsiella aerogenes X contains 5,312,129 bp scaffold length distributed over 32 scaffolds, containing 37 contigs totaling 4,662,216 bp, with a GC content of 54.90%. This genome will provide useful information for characterizing the molecular mechanisms associated with Sb resistance within the genus Klebsiella aerogenes X