Background: Integrons in Stenotrophomonas maltophilia are the major mechanism for trimethoprim/sulfamethoxazole (TMP/SMX) resistance. Molecular epidemiology of S. maltophilia with integrons has not been studied till now, and gene cassettes of the integron in S. maltophilia may change with time. Aim: Molecular typing and interrelatedness between TMP/SMX resistant S. maltophilia (TSRSM) isolates in a hospital in 2017 were analyzed and gene context of cassettes in integrons was studied. Methods: Molecular typing was determined through a multilocus sequence typing (MLST) scheme, while pulsed field gel electrophoresis (PFGE) was used for relatedness analysis of TSRSM with integrons. Mapping of gene cassettes in the integron was also performed through sequencing. Results: From 214 S. maltophilia isolates collected in 2017, 34 of them (15.9%) were TSRSM. A total of 20 (58.8%) from 34 TSRSM isolates harboring the class 1 integron were analyzed. The MLST analysis revealed 11 different sequence types, 5 out of which were novel STs (ST 830, ST 833, ST 836, ST 837, and ST 839), suggesting a wide genetic diversity. There were two clones with intrahospital dissemination between different hospital settings, according to PFGE. Mapping of gene cassettes of the integron revealed four novel combinations of multiresistance genes (aacA4 aadA5, aacA7 catB, cmlA10 aadA2, and aacA4 aphA15 catB3), indicating the continued evolutionary change of the gene cassettes. Conclusion: Evidence of clonal transmission within the hospital and continuous change of multiresistant gene combinations in the cassettes of the integron showed that S. maltophilia with resistance integrons may play a role in the spread of antimicrobial resistance.