Bolivia is a megadiverse country. A large part of its biodiversity is due to the fact that in its territory different biogeographical regions meet. As a preliminary means to understand how this biodiversity is being protected, three previous studies undertook an evaluation of how well represented the ecological regions were in the National System of Protected Areas (NSPA). However, the most recent biogeographical findings in Bolivia call for a new analysis of this sort. We try to achieve this, emphasizing the situation in the Andean dry regions, which have been given scarce priority, despite their high biological value. In general, xeric ecoregions are under-represented while humid ones are over-represented. The Prepuna and the central altiplano (which includes the Dry Puna sub-ecoregion) are not represented within the NSPA, nor is the Beni Cerrado sub-ecoregion. The Inter-Andean Dry Valleys cover only ca. 0.5% of the protected area, in spite of their diverse flora and status as one of Bolivia's most important centers or endemism. Although the diverse Chiquitos Dry Forest is well represented, it is protected mostly as an 'Integrated Management Natural Area', and thus lacks full protection. The Semi-Humid Puna and the Flooded Savannas of the Moxos Plains, important subdivisions of two main ecoregions, are markedly under-represented in the NSPA, despite the importance of Moxos plains as a center of endemism for birds. Other ecoregions have a representation in the NSPA which can be considered adequate or even excessive. The over-representation of the humid Yungas mountain forests seems to be justified as this is probably Bolivia's most important center of diversity and endemism. There is a need for a more proper distribution of some protected areas which consider true limits, size, diversity, endemism and other attributes of the different ecoregions in a more rigorous manner.