The development of analytical tools to determine the origin of fishes 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 analyses to study calcified structures of fishes (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 (<i>Arapaima</i> spp.) to evaluate their prediction potential to trace the fishes origin. Wild and farmed fish specimens, as well as food used for feeding pirarucu in captivity, were collected from different sites. Isotope composition of otoliths performed by isotope-ratio mass spectrometry (IRMS; <span classCombining double low line"inline-formula"><i>'</i>13C</span>) and femtosecond laser ablation multi-collector inductively coupled plasma mass spectrometry (LAfs-MC-ICPMS; <span classCombining double low line"inline-formula">87Srĝ•86Sr</span>) were compared to the isotopic composition of water and of the food given to the fishes 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&thinsp;% of correct classification for fish production (wild and farmed) and 76&thinsp;% of correct classification for the fish region. Classification accuracy for region varied between 100&thinsp;% and 29&thinsp;% for the Madeira and the Lower Amazon fishes, respectively. Overall, this preliminary trial is not yet fully developed to be applied as a commercial traceability tool. However, given the importance of <i>Arapaima</i> 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.