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Biduk-Biduk Karst Region has great potential to absorb and store organic carbon in vegetation and soil as well as to absorb inorganic carbon through the process of dissolution. The area has important economic value in supporting the REDD Program in Berau District. The purpose of this study is (1) to identify the amount of carbon stocks in various ecosystems; and (2) to identify the amount of carbon uptake in various ecosystems in the study area. Carbon stocks are computed based on four carbon sinks, i.e., above ground biomass, underground biomass, litter, and soil organic matter using the standard measurement method of SNI 7724: 2011. Carbon sequestration is calculated based on the input of carbon from the atmosphere to ecosystems through litter fall and karstification process and the output of carbon from the ecosystem to the atmosphere through soil respiration. Litter fall is measured using the litter trap method. Karstification is measured with standard limestone tablet method. Soil respiration is calculated with the closed chamber method. The results show that the ecosystems in the Biduk-Biduk Karst Region have a potential carbon stock of 4,800.92 tons/ha with the largest value in the secondary tropical forest of 732.6 tons/ha and the lowest value in the teak forest plantation of 358.2 tons/ha. Ecosystems in the Biduk-Biduk Karst Region have a potential carbon sequestration of 37.33 tons/ha/year with the largest contribution in the primary tropical forest of 7,63 tons/ha/year.