Abstract Attention to illegal logging practices and demanding policies in transnational timber trade have driven the need for species-level identification of timber. Historically wood has been identified to genus level using microscopy and anatomical characteristics, however, new chemometric and imaging methods have been developed to increase the speed and precision of timber identification. This study approaches species identification using a combination of complementary methods: Direct Analysis in Real Time–Time-of-Flight Mass Spectrometry (DART-TOFMS), wood anatomy, and fluorescence spectroscopy. Seven commercially and environmentally significant species in Pterocarpus , including P. erinaceus (CITES Appendix II), P. santalinus (CITES Appendix II), P. tinctorius (CITES Appendix II), P. indicus , P. macrocarpus , P. dalbergioides , and P. soyauxii were studied. It was found that DART-TOFMS paired with discriminant analysis of principal components (PCA) could classify species with an accuracy of 95–100%, while anatomy in combination with PCA applied to fluorescence spectra could be used to classify CITES Appendix II species. In the absence of access to DART-TOFMS, a combination of wood anatomy and fluorescence spectrometry can permit more accurate identification than anatomy alone.