Fish from both aquaculture and wild capture are exposed to veterinary and medicinal antibiotics (ABs). This study explored the occurrence and probable source of 46 antibiotic residues in muscle of farmed salmon and wild trout from Chile. Results showed that at least one AB was detected in all studied samples. Diverse patterns were observed between farmed and wild specimens, with higher ABs concentrations in wild fish. Considering antimicrobial resistance, detected ABs corresponded to the categories B (Restrict), C (Caution) and D (Prudence) established by Antimicrobial Advice Ad Hoc Expert Group (European Medicines Agency). Multivariate statistic was used to verify differences between farmed and wild populations, looking for the probable source of ABs as well. Principal components analysis (PCA) revealed that ciprofloxacin, moxifloxacin, enrofloxacin, amoxicillin, penicillin G, oxolinic acid, sulfamethoxazole, trimethoprim and clarithromycin were associated with wild samples, collected during the cold season. Conversely, norfloxacin, sulfaquinoxaline, sulfadimethoxine, nitrofurantoin, nalidixic acid, penicillin V, doxycycline, flumequine, oxacillin, pipemidic acid and sulfamethizole were associated with wild samples collected during the warm season. All farmed salmon samples were associated with ofloxacin, tetracycline, cephalexin, erythromycin, azithromycin, roxithromycin, sulfabenzamide, sulfamethazine, sulfapyridine, sulfisomidin, and sulfaguanidine. In addition, linear discriminant analysis showed that the AB profile in wild fish differ from farmed ones. Most samples showed ABs levels below the EU regulatory limit for edible fish, except for sulfaquinoxaline in one sample. Additionally, nitrofurantoin (banned in EU) was detected in one aquaculture sample. The differences observed between farmed and wild fish raise questions on the probable source of ABs, either aquaculture or urban anthropic activities. Further research is necessary for linking the ABs profile in wild fish with the anthropic source. However, to our knowledge, this is the first report showing differences in the ABs profile between wild and aquaculture salmonids, which could have both environmental and health consequences.