The purpose of this study was to type the Pseudomonas aeruginosa and Stenotrophomonas maltophilia isolates recovered from cystic fibrosis (CF) patients by random amplified polymorphic DNA (RAPD)-PCR and to determine the antibiotic susceptibility of these strains. P. aeruginosa (n=49), and S. maltophilia (n=11) isolates which had been recovered from 16 and 8 patients, respectively, during a 1-year period were investigated. Three primers were used for RAPD-PCR typing. Antibiotic susceptibility testing of all isolates was performed by the disc diffusion method. RAPD-PCR analysis revealed 21 (P. aeruginosa) and 9 (S. maltophilia) different genotypes. According to the antimicrobial susceptibility results, the P. aeruginosa and S. maltophilia strains were cumulated into 24 and 11 groups, respectively. The CF patients were colonized or infected with P. aeruginosa strains of single or sometimes multiple genotypes which remained stable over several months. Our results also revealed that cross-colonization might be possible among the patients who are followed up at the same center. Piperacillin-tazobactam for P. aeruginosa and trimethoprim-sulfamethoxazole for S. maltophilia were found to be the most active antibiotics according to our results.