Migratory marine species present challenges for conservation because of complex threats within their pelagic dispersal zones, including coastal foraging areas and extensive migration pathways, or at breeding grounds. To better understand the connectivity between green turtle rookeries and foraging populations, we sequenced the mtDNA control region of 987 turtles from 6 major foraging grounds on a ~2300 km longitudinal transect off eastern Australia, and used mixed stock analysis (MSA) to estimate their natal origins. We investigated variation in natal origins within different size classes and over spatial and temporal scales and compared this to approximately 30 yr of mark-recapture data. For adult turtles, we found that the northern Great Barrier Reef (nGBR) genetic stock dominated in the northern feeding grounds while the southern Great Barrier Reef (sGBR) and Coral Sea stocks dominated in the south, with a changeover of dominating stock occurring between 14° and 20° S. However, at the 3 most northern feeding grounds, we found an unexpected decrease (17-30%) in the proportion of nGBR turtles among small immature turtles relative to large immatures and adults. Four possible hypotheses were explored, with the 2 most plausible being that (1) small immature turtles from the sGBR and other rookeries first settle in nGBR feeding grounds, but later shift to other feeding grounds as they mature, or (2) a reduced hatching success for decades from the main nGBR rookery at Raine Island has resulted in reduced recruitment into the nGBR feeding ground from this stock. These results may indicate an alarming reduction in hatching success at the largest known green turtle rookery in the world.