This study was intended to address, in the field conditions of a rainbow trout farm, the effect of a flumequine treatment on the antimicrobial resistance of Aeromonas spp. isolated, during the production process, from different compartments (gut content and skin of treated fish, pond water and wall biofilm), and after the slaughtering process (36 days after the antimicrobial treatment end), from trout fillets destined to human consumption. Aeromonas were isolated on glutamate starch phenol-red selective agar supplemented or not with 8 mg/L of flumequine. Antimicrobial resistance patterns were defined by determination of minimal inhibitory concentrations of ten antimicrobial drugs, and bacteria with the same pattern were compared by pulsed-field gel electrophoresis (PFGE). Results indicated that this treatment effectively caused a transient increase of proportion of flumequine resistant Aeromonas in all compartments (production pond and fish). Their highest proportion was observed 24 h after the end of treatment, particularly in gut content and skin of trout and in pond biofilm. Resistant strains were still present 15 days after the end of treatment, particularly in the pond biofilm and fish skin. The antimicrobial resistance patterns of these strains showed a high diversity. Most strains were multidrug resistant, and some were resistant to quinolones and fluoroquinolones, streptomycin, oxytetracycline, chloramphenicol, florfenicol, sulfamethoxazole and trimethoprim. Multidrug resistant Aeromonas spp. clones characterized by their PFGE pattern were isolated in various compartments and/or at different sampling times, showing their capacity to persist and circulate in the trout farm environment and eventually end up, for a particular clone, on trout fillets ready for commercialisation