Using published IUCN red-lists for the threatened bird species of Indonesia (Stattersfield & Capper, 2000), we document that the species at risk in Indonesia are not a taxonomically random sample, consistent with patterns seen at the global scale (Purvis et al., 2000). This implies that a greater than random proportion of Indonesia's and the world's (through the loss of endemics) phylogenetic diversity (PD) is at risk (Von Euler, 2001). Using cytochrome b (Johns & Avise, 1998) and a distance-based taxonomy, we attempt to quantify this projected loss of PD in millions of years and conclude with a brief discussion of the conservation implications for Indonesia, and of the use of ‘evolutionary heritage’ as a measure for conservation at the geopolitical level.