The development of analytical tools to determine the origin of fish is useful to better understand patterns of habitat use and to monitor, manage and control fisheries, including certification of food origin. The application of isotopic procedures to study fish calcified structures (scales, vertebrae, and otoliths) may provide robust information about the fish geographic origin and environmental living conditions. In this study, we used Sr and C isotopic markers recorded in otoliths of wild and farmed commercialized pirarucu (Arapaima spp.) to evaluate their prediction potential to trace the fish origin. Wild and farm fish specimens, as well as food used for feeding pirarucu in captivity, were collected from different sites. Isotope analyses of otoliths performed by IRMS (δ13C) and LAfs-MC-ICPMS (87Sr/86Sr) were compared to the isotopic composition of water and of the food given to the fish in the farms. Wild fish specimens that lived in environments with the largest fluctuation of river water Sr isotope ratios over time presented the largest Sr isotope variations in otoliths. A quadratic discriminant analysis on otolith isotopic composition provided 58% of correct classification for fish production (wild and farmed) and 76% of correct classification for the fish region. Classification accuracy for region varied between 100% and 29% for the Madeira and the lower Amazon fishes, respectively. Overall, this preliminary trial is not yet fully satisfying to be applied as a commercial traceability tool. However, given the importance of Arapaima spp. for food security and the generation of economic resources for millions of people in the Amazon basin, further analyses are needed to increase the discrimination performance of these biogeographical tags.