Propolis is a natural substance produced by the bees to protect their hive. The present work reports the utilization of chemical profiling and fingerprinting combined with multivariate analysis for discrimination of the geographical origin of Malaysian stingless bee propolis. High Performance Thin Layer Chromatography (HPTLC) has been performed to profile the chemical composition of Geniotrigona thoracica propolis from different localities in East Coast of Peninsular Malaysia namely Besut, Terengganu (BST), Dungun, Terengganu (DGN), Lundang, Kelantan (LDG), Tanah Merah, Kelantan (TM) and Gua Musang, Kelantan (GM). The obtained HPTLC profiles showed the presence of flavonoids, phenolics and terpenoids in propolis. The chemical fingerprinting was obtained through Fourier Transform Infrared (FTIR) spectroscopy. Chemometric analysis on FTIR dataset using principal component analysis (PCA) and hierarchical cluster analysis (HCA) have classified the propolis into three major groups according to their sampling locations. Chemical fingerprinting analysis on the functional group via FTIR and chemometric revealed that the locations of propolis have direct correlation with the chemical composition, thus affecting the biological activities of propolis. Both chemical marker and chemical fingerprinting analysis are important tools in propolis standardization.