This study aims to determine the total phenolic content (TPC), total flavonoid content (TFC) and antioxidant activity of ethanolic extract propolis (EEP) and water extract propolis (WEP) derived from six Malaysian stingless bee species. The TPC and TFC were measured by Folin-Ciocalteu colorimetric and aluminium chloride methods, respectively. The antioxidant activity was determined by 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging assay. The results indicated that EEP of Geniotrigona thoracica had the highest TPC and TFC at 259.84 ± 4.97 mg/g GAE and 435.00 ± 6.57 mg/g QE, respectively. Similarly, EEP of G. thoracica exhibited the greatest free radical scavenging activity with the percentage of inhibition at 88.00 ± 13.34% and IC50 of 104.20μg/mL. Antioxidant activity was highly correlated with TPC (R2 = -0.744, p < 0.05) whereas no correlation was observed between TFC and antioxidant activity. This study indicates that the antioxidant property of the propolis extract may be influenced by elevated levels of phenolic content. In conclusion, ethanolic extract of G. thoracica is the greatest source of antioxidants among the six tested Malaysian stingless bee propolis and this suggests that the extract may serve as a promising source of antioxidant agent.