The heartwood of Acacia mangium is vulnerable to heart rot and this is the first study to investigate the role of heartwood extractives in its susceptibility. Acacia auriculiformis was compared with A. mangium because it is rarely associated with heart rot. The heartwood extracts of both species were dominated by three flavonoids (2,3-trans-3,4¢,7,8-tetrahydroxyflavanone, teracacidin, and 4¢,7,8,-trihydroxyflavanone), which were purified and identified by nuclear magnetic resonance spectroscopy. The latter compound has not been previously reported in A. mangium and evidence for melacacidin is also newly reported. The mass spectrometric (MS) behavior of these compounds is given, for example teracacidin does not form molecular ions by either electrospray ionization or atmospheric-pressure chemical ionization. The nature of Acacia tannins was compared to quebracho tannin (composed of profisetinidins) using oxidative cleavage to enable MS detection but a negative reaction was obtained for both, which suggests the Acacia tannins may also be of the 5-deoxy proanthocyanidin type. The concentration of flavanones was less when A. mangium heartwood was decayed but the amount of proanthocyanidins was only slightly reduced and therefore these compounds may be more resistant to degradation by heart rot fungi. We found that the total phenol content of A. auriculiformis was about fivefold that of A. mangium, and, while preliminary, this provides evidence for a role played by phenolic extractives in heart rot resistance of these Acacia species.