<p>Background: <em>Stenotrophomonas maltophilia (S. maltophilia)</em> is a multiple-antibiotic-resistant opportunistic pathogen that is being isolated with increasing frequency from patients with health-care-associated infections. <em>S. maltophilia</em> is inherently resistant to most of the available antimicrobial agents. Spread of resistant strains has been attributed, in part, to class I integrons. <em>In vitro</em> susceptibility studies have shown trimethoprim-sulfamethoxazole and new floroquinolones as two important agents with activity against these organisms.<br /> Methods: 150 isolates of <em>S. maltophilia </em>were isolated from clinical samples such as respiratory discharges, sputum, and catheter and hospital environments. These isolates were also subjected to susceptibility testing and polymerase chain reaction for four groups of genes including <em>int </em>encoding integron elements, <em>sulI</em> and <em>sulII</em> encoding trimethoprim-sulfamethoxazole resistance and <em>smqnr</em> encoding quinolone resistance.<br /> Results: The rate of resistance to trimethoprim-sulfamethoxazole was up to 27 (18%) and the highest resistance to quinolone family belonged to ofloxacin (20%) and the lowest rate was for gatifloxacin (16%). The results showed that 14% of isolates contained integron elements concomitantly with <em>sulI</em> and <em>sulII</em> genes.<br /> Conclusion: Resistance rate of <em>S. maltophilia</em> to co-trimoxazole and fluoroquinolones and detection of integron elements between isolates in this study showed that this rate corresponded to other data obtained from other studies.</p>