A genome-shuffled Stenotrophomonas maltophilia strain showing the enhanced ability of RDX degradation was constructed, and its characteristics were compared with those of the wild-type one. The shuffled strain was able to completely degrade 25, 50, and 75 µM RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) within 10, 30, and 50 days, respectively. However, it took 30 and 70 days for the wild-type strain to degrade 25 and 50 µM RDX, respectively, and at day 70, the strain degraded only 67% of 75 µM RDX. The shuffled strain reached its maximum growth at 50-60 days and exhibited approximately 1.5-fold increased cell numbers. SEM revealed more severe damage on the surface of the wild-type cells compared to the genome-shuffled cells. The mRNA levels of dnaK and groEL encoding the heat shock proteins were increased by 2.5-fold and fourfold, and DnaK and GroEL proteins were more highly produced in the shuffled cells. In addition, the mRNA levels of pnrB encoding a TNT nitroreductase, and algA involved in exopolymer biosynthesis, were slightly higher in the shuffled strain, but not as high as those of dnaK and groEL. These results indicate that the genome shuffling rendered the shuffled cells more resistant to RDX stress. A proteomic comparison revealed changes in the production levels of certain proteins including nitrate and cell protection, particularly those involved in metabolism. These proteomic analyses provide clues for understanding the improved RDX degradation by the genome-shuffled S. maltophilia strain.