Where high species richness and high human population density coincide, potential exists for conflict between the imperatives of species conservation and human development. We examine the coincidence of at-risk bird species richness and human population in the countries of the tropical Andes. We then compare the performance of the expert-driven Important Bird Areas (IBA) scheme against a hypothetical protected-areas network identified with a systematic reserve selection algorithm seeking to maximize at-risk bird species representation. Our aim is to assess the degree to which: IBAs contain a higher richness of at-risk species than would be expected by chance, IBAs contain more people than would be expected by chance, and IBAs are congruent with complementary areas that maximize species representation with an equivalent number of sites. While the correlation of richness and population was low for the region as a whole, representation of all at-risk bird species required many sites to be located in areas of high human population density. IBA sites contained higher human population densities than expected by chance (P < 0.05) and were markedly less efficient in representing at-risk bird species of the region than sites selected using the reserve selection algorithm. Moreover, overlap between IBAs and these latter sites was very limited. Expert-driven selection procedures may better reflect existing sociopolitical forces, including land ownership and management regimes, but are limited in their ability to develop an efficient, integrated network of sites to represent priority species. Reserve selection algorithms may serve this end by optimizing complementarity in species representation among selected sites, whether these sites are adopted independently or as a supplement to the existing reserve network. As tools of site selection, they may be particularly useful in areas such as the tropical Andes where complex patterns of species disjunction and co-occurrence make the development of representative reserve networks particularly difficult. Furthermore, they facilitate making spatially explicit choices about how reserve sites are located in relation to human populations. We advocate their use not in replacement of approaches such as the IBA initiative but as an additional, complementary tool in ensuring that such reserve networks are developed as efficiently as practically possible.