Identifying the origin of fish contained in a mixed fishery is critical for accurate stock assessments and the subsequent development of appropriate management strategies. Using a panel of 92 SNPs developed to differentiate Atlantic bluefin tuna (Thunnus thynnus) from the two main spawning areas (Gulf of Mexico and Mediterranean Sea), we used individual assignment to determine composition of feeding aggregations in the northwestern Atlantic Ocean (Gulf of Maine, Bay of Fundy, Scotian Shelf, Gulf of St. Lawrence, coastal Newfoundland). Among the 3,163 individuals collected between 2004 and 2018, we found that among lower age groups (<15 years) the spawning stock providing the most recruits to the Canadian fishery transitioned from Western Atlantic to Mediterranean origin over time. While the majority of older adults (>15 years) have consistently been of Western Atlantic origin, the disparity in the proportional contribution of western and eastern spawning groups narrowed significantly over the 14-year study period. Our results can be used to inform population-specific exploitation rates, improve stock assessments, identify age-dependent habitat use and areas suitable for additional conservation efforts.