Four xanthones, α-mangostin (1), β-mangostin (2), mangostenol (3), mangaxanthone B (4), three benzophenones, mangaphenone (5), benthamianone (6), congestiflorone (7) and one sterol, stigmasterol (8) were isolated from the stem barks of Garcinia mangostana L. and G. benthamiana (Planch. & Triana) Pipoly. Compounds 1, 2, 4 and 5 exhibited significant cytotoxicity through MTT assay towards MCF-7 and MDA-MB-231 cells with the IC50 values range from 4.4 to 12.0 µM. Remarkably, mangaphenone (5) showed non-cytotoxicity against normal Vero cells, revealing its potential as lead compound for anti-breast cancer drug. Structure-activity relationship postulated that the prenyl and hydroxyl groups present in xanthones are important in promoting anti-proliferative effects. Molecular docking simulation study of 1, 2, 4 and 5 with 2OCF and 4PIV implied that the induction of apoptosis for both cancer cells involve ER and FAS signaling pathways. Future study on the lead optimization of 5 is highly recommended.