The large organic matter flow in tropical coastal areas is recognized as an important process in the global carbon (C) cycle.However,the nature of organic matter flow in semi-enclosed tropical estuaries remains unclear due to the various environmental processes (tidal change,river flow,waves from the sea,and internal circulation) and organic matter sources therein.Thus,sediment organic matter (SOM) sources,and their distribution pattern,are key to understanding ecosystem material flow.Our research in the Batan Bay Estuary,Philippines,a semi-enclosed estuary under large mangrove deforestation,was conducted to determine ecosystem properties through analysis of C and nitrogen stable isotope ratios and environmental factors.First,we determined that mangrove litter,microphytobenthos,and phytoplankton are the main SOM sources in the Batan Bay Estuary.Second,the estuary was classified into three ecological zones (the Bay zone,Back-barrier zone,and River zone).In addition,we estimated SOM source ratios using the Stable Isotope Analysis in R package and determined different organic matter sources in different zone.The high ratios of mangrove litter as SOM indicate that a large amount of terrestrial plant organic matter remains despite the heavy mangrove deforestation that has occurred since the 1980s,and that the Back-barrier zone consists of a different type of ecosystem that promotes accumulation of C from mangrove litter and microphytobenthos.