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In order to find the simple biochemical markers for selection of mangrove clones with high carbon sequestration, This work was made in two species (Rhizophora mucronata and Avicennia marina) under two seasons by analysing the carbon sequestration rate in mangrove biomass, in relation to 15 biochemical fractions- carotenoids, anthocyanins, flavonoids, phenols, tannins, leaf wax, chloroplast, chlorophylls (a, b, a/b, total) and chloroplasts. Carbon sequestration rate was positively correlated with chlorophyll a, b, total, flavonoids, leaf surface wax and chlorophyll an of the chloroplast. Anyone of these biochemical markers is suggested for selecting the mangrove clones of high carbon sequestration potential. Keywords: Mangroves, Rhizophora mucronata and Avicennia marina, Carbon sequestration, Biochemical markers