More biodiversity could be protected in situ if the few species that attract the most popular support (the ‘flagship’ species) had distributions that also covered the broader diversity of organisms. We studied how well different groups of mammals performed for representing the diversity of mammals and breeding birds among 1° areas of sub-Saharan Africa. We demonstrate that choosing areas of sub-Saharan Africa using either conservationists' six primary flagship mammals, or the six ‘Big Five’ mammals popular with wildlife tourists, is not significantly better for representing the diversity of mammals and birds than choosing areas at random. Furthermore, neither of these groups is significantly better for representing the diversity of mammals and birds than groups of the same number of species chosen at random. We show that in order to succeed in representing many mammals and birds in area selection, it is not sufficient for the groups used for selection to occur in many different eco-regions, they must also have low overlaps in distribution, so as to provide high ecological complementarity (a similar pattern of ecological complementarity must be shared by the larger group of species to be represented). Therefore there may be a need for an explicit policy to balance the requirements of flagship conservation and broader biodiversity conservation, which will have implications for the distribution of resources.