The development of traceability methods to distinguish between farmed and wild-caught fish and seafood is becoming increasingly important. However, very little is known about how to distinguish fish originating from different farms. The present study addresses this issue by attempting to discriminate among intensively farmed freshwater Murray cod originating from different farms (indoor recirculating, outdoor floating cage, and flow through systems) in different geographical areas, using a combination of morphological, chemical, and isotopic analyses. The results show that stable isotopes are the most informative variables. In particular, delta(13)C and/or delta(15)N clearly linked fish to a specific commercial diet, while delta(18)O linked fish to a specific water source. Thus, the combination of these isotopes can distinguish among fish originating from different farms. On the contrary, fatty acid and tissue proximate compositions and morphological parameters, which are useful in distinguishing between farmed and wild fish, are less informative in discriminating among fish originating from different farms.