Understanding population connectivity is paramount for effective conservation. While genetic tools have elucidated sea turtle migration patterns, notable data gaps limit our understanding of ocean-wide connectivity, especially regarding east Atlantic green turtles. We characterized the genetic composition of a globally important green turtle foraging aggregation at the Banc d’Arguin, Mauritania, incorporating data from 323 individuals captured between 2018 and 2021. Using extended mitochondrial DNA D-loop (738 base pairs [bp]) and mitochondrial short tandem repeat (mtSTR; ~200 bp) markers, we assessed the genetic structure of Atlantic green turtle foraging aggregations and estimated the most likely origin of immature green turtles from the Banc d’Arguin using mixed stock analyses (MSAs). We identified 6 D-loop haplotypes, with a clear dominance of CM-A8.1 (91.8%) followed by CM-A5.1 (6.3%) and 4 rare haplotypes: CM-A1.4, CMA6.1, CM24.1 and CM36.1. We found 13 mtSTR haplotypes, with ‘7-12-4-4’ being dominant (89.0%). The genetic composition at the Banc d’Arguin differed significantly from the only foraging aggregation studied in West Africa to date—in the archipelago of Cabo Verde (located ca. 750 km from the Banc d’Arguin)—dominated by haplotype CM-A5. The MSA combining both genetic markers indicated that 87.6% of immature green turtles at the Banc d’Arguin originate from the major East Atlantic rookery at Poilão (Guinea-Bissau), but 11.6% come from more distant rookeries in South America (8.1%) and potentially Ascension Island (3.4%). We suggest that green turtle transatlantic movements may be more common than previously thought and highlight the importance of the Banc d’Arguin as a regional foraging hub for this species.