Background: Stenotrophomonas maltophilia (S. maltophilia), is a remarkable nosocomial pathogen, packed with different intrinsic mechanisms of resistance to most antimicrobials. Trimethoprim/Sulfamethoxazole (SXT) is the treatment of choice for S. maltophilia infections. However, different acquired factors may render SXT ineffective. Our aim was to investigate the susceptibility pattern to levofloxacin (LEV) and minocycline (MIN) among SXT non-susceptible isolates, as well as the different expression levels of different efflux pumps.   Methods: Susceptibility pattern to LEV and MIN was investigated as well as the expression level of different efflux pumps SmeABC, SmeDEF and SmrA and the presence of smqnr and tetM. Results: Among the 19 SXT non-susceptible isolates, 57.89% were susceptible to LEV and 10.52% were susceptible to MIN. It was found that 68.42%, 15.78% and 36.84% of the isolates showed over-expressed SmeABC, SmeDEF and SmrA, respectively. The results showed no significant correlation between over-expression of efflux pumps and resistance to LEV and MIN. Moreover, smqnr was detected in 4 out of 8 LEV non-susceptible isolates, while tetM was present in 11 out of 17 MIN non-susceptible isolates. Conclusion: As far as previously reported, this is the first study dedicated to SXT non-susceptible S. maltophilia isolates, that reported the presence of tetM and smqnr and the over-expression of SmeABC, SmeDEF, and SmrA among clinical isolates in Alexandria, Egypt. The findings emphasize that LEV can be used as a suitable option in managing S. maltophilia infections.