Honey is the world’s third most adulterated food. The addition of cane sugar or corn syrup and the mislabelling of geographic origin are common fraudulent practices in honey markets. This study examined 100 honey samples from Australia (mainland and Tasmania) along with 18 other countries covering Africa, Asia, Europe, North America and Oceania. Carbon isotopic analyses of honey and protein showed that 27% of commercial honey samples tested were of questionable authenticity. The remaining 69 authentic samples were subject to trace element analysis for geographic determination. One-way ANOVA analysis showed a statistical difference (p < 0.05) in trace element concentrations of honey from Australian regions and different continents. Principal component analysis (PCA) and canonical discriminant analysis (CDA) coupled with C5.0 classification modelling of honey carbon isotopes and trace element concentrations showed distinct clusters according to their geographic origin. The C5.0 model revealed trace elements Sr, P, Mn and K can be used to differentiate honey according to its geographic origin. The findings show the common and prevalent issues of honey authenticity and the mislabelling of its geographic origin can be identified using a combination of stable carbon isotopes and trace element concentrations.