Abstract The physicochemical parameters, sugars, minerals and volatile compounds were selected in current work as the crucial parameters for evaluating multifloral honeys produced by Apis cerana cerana Fabricius, Apis dorsata Fabricius and Lepidotrigona flavibasis Cockerell. A summarized physicochemical profile of multifloral honeys exhibited great variability, which was quite different from that of A. mellifera honey, regarding color (83.86–328.36 mmPfund), ash (0.30–0.34 g 100 g−1), soluble solid (74.72–80.41 °Brix), diastase activity (5.48–6.70 °Gothe), electrical conductivity (0.40–0.55 mS cm−1), free acidity (0.51–0.85 mol kg−1), hydroxymethylfurfural (0–39.28 mg kg−1), moisture (18.65–23.80%) and pH (3.73–3.95). Fructose and glucose were the major carbohydrates in Apis spp. honeys but high level of maltose was present in L. flavibasis honey. The potassium, zinc and calcium were abundant elements in multifloral honeys. The principal component analysis was applied to discriminate honeys from different bee species by cobalt, sulfur, magnesium, color, maltose, pH, free acidity, potassium, molybdenum, F/G, HMF and iron, and it was concluded that L. flavibasis honey had better quality compared to the other honeys. Moreover, the specific volatile compounds detected in A. dorsata and L. flavibasis honeys were more than A. cerana cerana honey, which could be used as the characteristic markers discriminating honey samples.