Physicochemical and antioxidant properties of raw honeys from Malaysia were used as markers for determining its entomological source of bee species of Apis dorsata, Apis mellifera, Apis cerana, or Heterotrigona itama. Physicochemical properties of moisture content, water activity, specific gravity, viscosity, pH, free acidity, electrical conductivity, colour (L*, a* and b*), colour intensity, and antioxidant properties including the DPPH free radical scavenging activity power (1/IC50), ascorbic acid equivalent antioxidant content (AEAC), ferric ion reducing antioxidant power (FRAP), and total phenolic content (TPC) were measured and analysed. Honeys were classified into two major groups of those from honey bees (Apis spp.) and Trigona stingless bees (Heterotrigona itama) from its physicochemical and antioxidant properties using hierarchical cluster and principal component analyses. The Kelulut honey produced by stingless bees, Heterotrigona itama was differentiable from honeys from the regular honey bee species, the Apis spp. with characteristics of high moisture content of 33.24 g/100 g, free acidity of 136.8 meq/kg, colour intensity of 990.3 mAU, AEAC of 26.64 mg/100 g, and FRAP of 41.95 mg AAE/100 g. Honey classification by its entomological origin helps in honey identification and it reduces honey fraudulence.