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Coastal seagrass habitats are critical foraging grounds for endangered green turtles (Chelonia mydas). However, these habitats are vulnerable to anthropogenic effects, potentially leading to their degradation with consequent impacts on the health status of foraging green turtles.Two foraging habitats of green turtles in Tun Mustapha Park, Sabah, Malaysia were surveyed: Kudat Mainland and Balambangan Island, by capturing green turtles and evaluating their physical body condition as well as assessing seagrass cover.Despite having similar genetic compositions, the Kudat Mainland aggregation had significantly higher body size (curved carapace length: 61.7 ± 14.5 cm, body weight: 30.0 ± 22.2 kg), Fulton's body condition index (BCI: 1.49 ± 0.13), barnacle (Chelonibia testudinaria) occurrence (78.8%) and barnacle abundance (5.46 ± 9.90 barnacles/turtle) than the Balambangan Island aggregation (curved carapace length: 51.6 ± 8.1 cm, body weight: 17.3 ± 7.7 kg, BCI: 1.40 ± 0.09, barnacle occurrence: 31.0%, barnacle abundance: 0.50 ± 0.92 barnacles/turtle). The differences in BCI between the nearby aggregations could not be attributed to size and barnacle occurrence differences, suggesting the foraging habitat is the primary factor affecting the body condition of green turtles.Seagrass cover at Kudat Mainland was only slightly higher than at Balambangan Island. These findings suggest that the body condition of green turtles is potentially sensitive to the quality of foraging habitats such as nutrients and water quality.It is crucial to monitor the health of foraging habitats and their impact on the body condition of turtles. It is recommended that habitat‐turtle dynamics are given conservation priority, in parallel to water quality monitoring – with action taken to reduce pollution if necessary. A holistic approach to turtle conservation is therefore required. [ABSTRACT FROM AUTHOR]