<p>Two new types of anthocyanidins, mopanidin (<b>1</b>) and peltogynidin (<b>2</b>) were isolated from the heartwood of <i>Peltogyne mexicana</i> for the first time. The structures of the isolated compounds were determined using NMR and MALDI-TOF MS analysis. These pigment compounds had flavylium moiety and oxymethylene bridge between B and C ring (D ring), and resorcinol moiety as B ring. The result of the monitoring of the oxidation of pigment precursors, it was clarified that <b>1</b> and <b>2</b> were generated from (+)-mopanol and (+)-peltogynol, respectively. The compounds were considered to be produced by light and oxygen in a different way from common anthocyanidins. Compared to cyanidin, which has similar structure except D ring, <b>1</b> and <b>2</b> showed an additional absorption around 560–570&#xa0;nm to show more blueish purple. In addition, they showed more stability than cyanidin in neutral and acidic condition. Considering the result of in silico calculation of their dihedral angles consisting of the AC and B rings, <b>1</b> (<i>θ</i> = 174.4º) and <b>2</b> (<i>θ</i> = 172.0º) had a nearly planar structure, while cyanidin had a twisted structure (<i>θ</i> = 154.2º). It was suggested that the bulkiness around C-2 due to the nearly planar structure in <b>1</b> and <b>2</b> contributed to their relatively color stabilities in neutral condition. These findings provide insight into the structural features influencing pigment stability and color change mechanism of <i>P. mexicana.</i></p>