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Sea turtles are marine reptiles that undertake long migrations through their life, with limited information regarding juvenile stages. Feeding grounds (FGs), where they spend most of their lives, are composed by individuals from different natal origins, known as mixed stock populations. The aim of this study was to assess genetic composition, natal origins and demographic history of juvenile green turtles (Chelonia mydas) at the Paranaguá Estuarine Complex (PEC), Brazil, considered a Natural World Heritage site. Tissue samples of stranded animals were collected (n = 60), and 700 bp mitochondrial DNA sequences were generated and compared to shorter sequences from previously published studies. Global exact tests of differentiation revealed significant differences among PEC and the other FGs, except those at the South Atlantic Ocean. Green turtles at PEC present genetic signatures similar to those of nesting females from Ascension Island, Guinea Bissau and Aves Island/Surinam. Population expansion was evidenced to have occurred 20–25 kYA, reinforcing the hypothesis of recovery from Southern Atlantic refugia after the last Glacial Maximum. These results contribute to a better understanding of the dynamics of green turtle populations at a protected area by providing knowledge on the dispersion patterns and reinforcing the importance of the interconnectivity between nesting and foraging populations.