Background: Pseudomonas aeruginosa is a major human pathogen, which also affects animals. It is thought that P. aeruginosa has a non-clonal epidemic population structure, with distinct isolates found in humans, animals or the environment. However, very little is known about the structure of the P. aeruginosa population from diseased animals. Data on antimicrobial resistance are also scarce. Results: Thirty-four already registered and 19 new MLST profiles were identified. Interestingly, a few clones were more prevalent, and clones associated to human outbreaks were also detected. Multidrug resistance phenotypes were overall rare. Conclusion: We highlight the non clonal structure of the population and show a higher prevalence of specific clones, possibly correlating with higher pathogenicity. The low proportion of antimicrobial resistance contrasts with the high resistance rate of human isolates.