Isolation and characterization of antigastric cancer bioactive compound berberine from Ceriops decandra mangrove plant species are reported. The plant is used in fisherman community as folklore medicine and exhibits antioxidant and anticancer activity, but active components present in the plant are unclear. Berberine has been isolated from n-butanol extract of C. decandra through column chromatography and checked by TLC, preparative HPLC, HPLC, NMR and mass spectroscopy. Preparative HPLC fraction of dried n-butanol extract of C. decandra was dissolved in water–methanol (1:1 v/v) mixture and subjected to preparative scale HPLC in order to isolate active compounds. The collected product was evaporated to dryness under vacuum and analyzed by HPLC, NMR and mass spectroscopy. The fraction collected from preparative HPLC showed a chromatogram peak at a retention time of 10.98 min, the same as that of berberine standard. The compound isolated from C. decandra n-butanol extract exhibits a molecular ion peak at m/z 336.12 as the base peak and other peaks at 290, 262, 248, 204 and 192 [M +H+], corresponding to molecular formula C20H18NO4 confirmed by gas chromatography/mass spectroscopy. The obtained berberine exhibits potent antigastric cancer activity and can be used as innovative product. © 2021, Springer Science+Business Media, LLC, part of Springer Nature.