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The utility of spatial conservation prioritization (SCP), could be limited by the biases produced by taxonomic uncertainty and by the lack of an accepted taxonomic checklist for a diverse group of species. Using information on the endemic cacti of the Atacama Desert and Mediterranean Chile, we assessed the implications for SCP of the existence of two contrasting taxonomies. Biological and socioeconomic criteria were combined to design conservation networks for two widely used taxonomic checklists of endemic Chilean cacti. We analyzed the spatial distribution of these conservation networks to assess the congruence of the taxonomic checklists and evaluated whether our models match the geographic distribution of the National System of Protected Areas. The conservation networks had low similarity. However, consensus scenarios revealed several coincident priority sites. Gap analyses indicated that one-third of the species were completely unprotected but that all species were satisfactorily protected in the consensus scenario. Consensus scenarios based on different checklists can improve SCP because this approach is less affected by taxonomic uncertainty. It is more conservative (without a priori taxonomic decisions) and robust (priority sites are supported by more than one scenario). Given the narrow distribution of cacti, effective conservation actions demand environmental actions in a geographically explicit framework. (C) 2014 Elsevier Ltd. All rights reserved.