Five flavonoids, one isoflavone and five xanthones were isolated from Anaxagorea luzonensis. Of these eleven isolated compounds, 1,3,5-trihydroxy-4-prenylxanthone (3) was a relatively potent inhibitor of phosphodiesterase type 5 (PDE5), with an IC50 value of 3.0 μM. This is the first report showing that natural xanthones can exhibit promising PDE5 inhibitory activity. Moreover, this study revealed that the presence of the C-4 prenyl residue attached to the xanthone core is correlated with the significant PDE5 inhibitory activity.