Despite providing valuable ecosystem services, mangroves are endangered under the recent global natural as well as anthropogenic changes. Conservation of mangroves is now one of the pillars of Sustainable Development Goals (SDG) 2030. An assessment of mangrove is essential before initializing any conservation strategy. This paper aimed to assess the ecosystem conditions of mangroves and the relative changes in ecosystem conditions from the natural background under different scales of anthropogenic interruption in Okinawa Prefecture, Japan. To assess mangrove’s ecosystem condition, foliar stable nitrogen isotope ratio (δ15N) of mangroves is used as ecosystem monitoring indicator. Whereas, a difference index (DI) of mangrove foliar δ15N is established to compare the relative deviation in ecosystem conditions of anthropogenically impacted mangroves from reference mangroves. Results showed that the mean foliar δ15N values of Bruguiera gymnorrhiza, Kandelia obovata, and Rhizophora stylosa on Okinawa Island (Is.) are 5.12 ± 2.32‰, 7.54 ± 2.85‰ and 7.09 ± 3.29‰, respectively, on Iriomote Is., 1.83 ± 1.93‰, 2.01 ± 0.31‰ and 1.04 ± 2.38‰, respectively, and on Ishigaki Is., foliar δ15N values of Bruguiera gymnorrhiza and Rhizophora stylosa are 5.23 ± 3.33‰ and 6.00 ± 3.63‰, respectively. A range of negative to positive values from -0.54 to 3.66 of DI indicates different level of changes in ecosystem conditions of the mangroves compared to the reference sites, which is set at zero. A significant negative correlation between DI values and the forest area ratio of the watersheds has been observed. It indicates that the forest cover is the driver of maintaining pristine condition of an ecosystem. Findings of the study recommended that Todoroki and Manko mangrove watersheds in Okinawa, Japan should be taken into consideration for necessary conservation on priority basis.