A study was conducted to isolate, identify alkaloid content of Rhizophora mucronata and to determine its effectiveness of methanol extract against barnacles. The use of tributyltin (TBT) was effective to reduce biofouling. However, TBT has been prohibited because they are detrimental to non-target organisms and for surrounding environment. Rhizophora mucronata is useful as antifouling compounds because of the secondary metabolites. Its active compound will replace TBT as it is safe against the biota and the marine environment. The root’s bark, trunk’s bark and leaves powder were macerated using methanol. The methanol extract was used for total alkaloid isolation. The separation of alkaloids was done by preparative TLC and analyzed with FTIR and LC-MS. The results showed that the alkaloid metabolite identified was benzamide (C17H14N2O2). The methanol extract had antifouling activity against barnacles. The highest yield was found in Rhizophora mucrophora leaf extracts at about 24.8%. Antifouling activity test against barnacles showed that a mixture of wood paint and Rhizophora mucronata leaf, root and bark extracts were not significantly different.