An understanding of population dynamics is needed to assess the viability of migratory species. Monitoring of marine turtles at foraging grounds may detect changes in population trends that would take decades to be seen at nesting beaches. Mixed Stock Analysis using molecular markers provides a tool for estimating the origin of turtles sampled at foraging grounds. Here, we analysed mitochondrial DNA sequences of 90 immature green turtles at 2 foraging grounds in northwestern Sabah, Malaysia. We used data from 30 Indo-Pacific green turtle rookeries as the baseline for tracing the origin of turtles at the 2 foraging grounds. The inferred origins of turtles at the 2 locations were not different and indicated that the majority originated from 3 major populations in Southeast Asia, the Turtle Islands of Sarawak in northwestern Borneo (29%), the Turtle Islands Heritage Protected Area (TIHPA) (28%) and Peninsular Malaysia (25%). Previous analyses indicated a 1:4 female-biased sex ratio at the foraging grounds, and based on our results, this largely reflects the use of unshaded beach hatcheries at some of the source rookeries for decades, which resulted in mostly female hatchlings. This result is supported by differences in the origins of male and female turtles. The result suggests a greater proportion of males originating from Peninsular Malaysia and fewer males originating from Sarawak and possibly the TIHPA compared to females. We discuss the implications of hatchery practices that influence sex ratios of hatchlings and recommend future research to improve the management of marine turtles in the region.