Conservation biogeography involves the application of biogeographical principles and methods to conservation issues, including the design of protected areas. Bioregionalisation has been central in the implementation of main global conservation strategies, providing the basis for prioritising protected areas and evaluating their representativeness and effectiveness in conservation actions. Traditionally, experts established these bioregionalisations without repeatable methodologies and using only qualitative evidence, which has set constraints in their usefulness. We compared three descriptive bioregionalisations commonly used for conservation decision-making, with a regionalisation produced using quantitative methods (endemicity analysis), so as to assess biases and differences in the representativeness of the existing protected-area system of Argentina. Areas of endemism were detected using NDM/VNDM quantitative methodology on a database consisting of 19 250 distribution records of 116 taxa of snakes, and the results were compared with previous descriptive regionalisations. We recovered 9 quantitative bioregionalisation units (QBU) v. 6–8 descriptive bioregionalisation units (DBU) proposed by previous authors. From this comparison, the following was found: (1) we discovered three new QBU not considered by any previous DBU; (2) other three areas proposed by DBU are not supported by our endemicity analysis; (3) we detected differences comparing the representativeness of protected areas between descriptive v. quantitative bioregionalisations, leaving the first, some areas of conservation relevance largely unprotected. Moreover, DBU were characterised by a high degree of uncertainty and biases, such as the consideration of probably artificial units, the non-recognition of some natural units and mistakes in the representativeness of protected areas. We emphasise the importance of applying quantitative biogeographic methods to identify bioregionalisation units and its fundamental role in conservation biogeography so as to optimise protected-area efficiency and other territorial conservation strategies.