Representativeness is a desirable property of conservation networks. In this paper an attempt is made to assess the efficiency of current conservation networks in Portugal in representing vertebrates (reptiles and amphibians) and plants (gymnosperms, pteridophytes and bryophytes). It was found that whilst the protected areas do not sample all species in the database they provide a better result than choosing areas at random. For the goal of maximizing representation of taxa per unit area hotspots and complementarity performed better. A pattern of over-representation of vertebrates in relation to lower plants was discovered among selected conservation areas in Portugal suggesting that charismatic organisms with large home ranges may not always be the most appropriate surrogates for biodiversity when representativeness is sought. When trying to fill the gaps in current protected areas with additional areas only complementarity performed better than choosing areas at random. Both rarity and richness hotspots gave worse results. Opportunistic administrative criteria such as supplementing the PAS with other conservation areas (CORINE Biotopes) without taking into account their contribution to a representation goal was nearly half as good as choosing areas at random. The results recall for the need of explicit goals and accountable methods in area selection for conservation and reinforce the role of complementarity for finding additional areas to protected areas when limited resources are available for ‘in situ’ conservation.