Qualitative screening of multiclass secondary metabolites present in the fruits, leaves and stem bark extracts of Garcinia travancorica was carried out using HPLC-QTOF-MS analysis. Twenty-three compounds were identified in the fruits, leaves and stem bark; including two acids (hydroxycitric acid and hydroxycitric acid lactone), eight biflavonoids (morelloflavone, GB-1, GB-la, GB-2, GB-2a, fukugiside, xanthochymusside and GB-la glucoside), nine xanthones (α-mangostin, γ-mangostin, 1,5-dihydroxy-3-methoxyxanthone, garciniaxanthone E, 4-(I,1-dimethylprop-2-enyl)-1,3,5,8-tetrahydroxy-xanthone, garcinone A, garcinone B, garcinone C and polyanxanthone C) and four polyisoprenylated benzophenones (gambogenone, aristophenone A, garcinol and garciyunnanin A). Cytotoxicity studies of the major biflavonoid fukugiside reported from G. travancorica leaves revealed a dose-dependent cancer cell growth inhibition in A431 and HeLa cells. The antiproliferative effect appears to be due to the ability of fukugiside to induce S-phase arrest and apoptotic cell death. In HeLa cells, fukugiside reduced the expression of MAPKp38 by 26.1% compared with untreated control.