Pseudomonas aeruginosa is the major pathogen in the cystic fibrosis (CF) lung, the predominant source of its acquisition, however, is under discussion. In order to study the molecular epidemiology, we evaluated 86 P. aeruginosa isolates from 43 CF patients from southeast Austria. The DiversiLab system was used to identify genetic relationships among the isolates. Antibiotic susceptibilities were tested with a broth microdilution method (Micronaut Merlin). A total of 39 unrelated P. aeruginosa genotypes were found of which 34 were unique to a single patient and one was unique to a sibling pair. We found low rates of resistance for β-lactams with resistance to piperacillin/tazobactam and ceftazidime ranging from 4 to 6%. Resistance rates for meropenem and ciprofloxacin were 11% and 15%, respectively. The prevalence of multidrug-resistant isolates was 2%. We conclude that the majority of P. aeruginosa isolates from CF patients originate from environmental sources and patient-to-patient spread is very uncommon in our centre.