The Pantanal is the world's largest contiguous freshwater wetland spanning Brazil, Bolivia, and Paraguay. It contains the greatest wildlife densities in the Neotropics and was enlisted by all three countries in the Ramsar convention on wetland conservation. The Brazilian government, together the UNESCO's Man and the Biosphere Program, declared a biosphere reserve in the Pantanal in 2000. Other plans to protect the region include expansion of existing reserves and land use regulations following recommendations from the Cerrado-Pantanal priority setting workshop. Here we evaluated how four conservation scenarios complied with the principles of systematic conservation planning and analyzed their representativeness, efficiency, and complementarity using 17 vegetation classes as surrogates for regional biodiversity. We used MARXAN (systematic conservation planning software) to determine the value of the habitat types protected by each conservation scenario. We found that none of the four conservation scenarios met preferred areal targets for protection of habitats, nor did any protect all 17 biodiversity surrogates. The Pantanal Biosphere Reserve provided the best compromise in conservation planning.