The chemical compounds found in propolis vary according to plant sources, species, and geographical regions. To date, Indonesian propolis has not yet become standardized in terms of its chemical constituents. Thus, this study aimed to identify the presence of marker compounds and determine whether different classes of Indonesian propolis exist. In this study, yields, total polyphenol content (TPC), total flavonoid content (TFC), and antioxidants were measured. Identification of chemical compounds was carried out with Fourier-transform infrared (FTIR) spectroscopy and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Metaboanalyst 6.0 was employed in conducting principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) using the results of the FTIR and LC-MS/MS. The propolis with the highest TFC, TPC, and antioxidant activity was Geniotrigona thoracica from North Sumatra. The results of propolis compound mapping based on region with discriminant analysis revealed that types of propolis from Java have similar characteristics. Then, based on species, the types of propolis from Tetragonula laeviceps and Heterotrigona itama have special characteristics; the samples from these species can be grouped according to similar characteristics. In conclusion, 10 potential marker compounds were identified in Indonesian propolis, enabling regional and species-specific varieties of Indonesian propolis to be classified based on chemical composition mapping.