Honey produced by three stingless bee species (Melipona flavolineata, M. fasciculata and Apis mellifera) from different regions of the Amazon was analyzed by separating phenolic acids and flavonoids using the HPLC technique. Data were subjected to multivariate statistical analysis (PCA, HCA and DA). Results showed the three species of honey samples could be distinguished by phenolic composition. Antioxidant activity of the honeys was determined by studying the capacity of inhibiting radicals using DPPH assay. Honeys with higher phenolic compound contents had greater antioxidant capacity and darker color.