Phytochemical investigation through cytotoxicity bioassay-guided isolation of Geniotrigona thoracica propolis led to the identification of five cycloartane-type triterpenes, including mangiferonic acid 1, ambonic acid 2, mangiferolic acid 3, ambolic acid 4 and cycloartenol 5. Their structures were established based on detailed spectroscopic analysis and comparison with literature data. Compounds 1-5 were isolated for the first time in this species. From cytotoxicity MTT assay, compound 3 inhibited the growth of breast (MCF-7) and hepatocellular carcinoma (HepG2) cancer cell lines with IC50 of 5.08 and 4.82 µg/mL, respectively. Cytotoxicity of compounds 1-5 were reported for the first time against HepG2 cancer cell lines. Compounds 1-4 were suggested to serve as main and/or analytical markers for G. thoracica propolis based on HPLC analysis. To our knowledge, this is the first report on the isolation of bioactive constituents and identification of chemical markers for G. thoracica propolis.