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Assessments of fisheries by‐catch on marine megafauna are important for developing effective management strategies. For sea turtles, impacts may be evident in nesting population trends, but generally only after a lag, as turtles are slow to mature. We examined 850 loggerhead turtle (Caretta caretta) by‐catch samples collected over 14 years throughout the western North Atlantic to identify source nesting populations. We identified proportions of turtles from 19 distinct management units (MUs), using mitochondrial DNA and mixed stock analysis, considering population size. We found a significant split in the distribution of small versus large loggerheads to the north and south of Cape Hatteras, North Carolina (latitude 35°N). North of Cape Hatteras, large turtles came from south‐east Florida (SEFL; 44% ± 15%) and the northern United States (33% ± 16%) MUs, while south of Cape Hatteras, the major contributors were Central East Florida (52% ± 20%) and south‐east Florida (SEFL; 41% ± 20%). Small turtles in the north came from Central East Florida (64% ± 14%), and in the south, south‐east Florida had the highest representation (56% ± 25%). There was little contribution from Mediterranean and Cape Verde populations, indicating low risk from western North Atlantic by‐catch to MUs in the Mediterranean. Understanding where threats may impact source populations is important, particularly for larger size turtles, as these individuals have the highest reproductive value. These findings allow more informed threat assessments to be conducted for loggerhead turtles considering spatial and demographic structure.