Hotspot identification is a crucial strategy for setting conservation priorities. Since both the total number of species and the number of endemic species tend to increase with area, prioritizing sites according to their overall species richness or endemic species richness can produce rankings that simply mirror the sizes of the sites. Thus, it is important to control for the dependence of species number on site area. For this reason, some authors have proposed that the species–area relationship (SAR) and/or the endemics–area relationship (EAR) should be modelled and then the sites located above the fitted curve(s) (i.e. those having positive residuals) designated as hotspots. However, (1) there may be large uncertainties about which model provides the best fit to the SARs/EARs, (2) the use of residuals may lead to sites being identified as hotspots when they only have very few species and (3) there is no guarantee that the sites selected as hotspots by the SAR really include a large fraction of the overall diversity. Thus, it is important to evaluate the ability of the hotspots designated by these procedures to really conserve total and endemic species diversity; the best strategy may in fact be to use a combination of approaches.