The taxonomic criteria used as bases for endangered species lists can affect conservation policy decisions. We emphasize that the use of different taxonomic units affects the baselines of such lists. Recent taxonomic reviews for the Mexican avifauna provided the tools for assessing this effect on a highly diverse avifauna which is currently in need of serious conservation actions. Most ornithologists have used a taxonomy based on the biological species concept (BSC) to make decisions on species limits and therefore to set them into endangered species lists. However, the application of the phylogenetic species concept (PSC) as an alternative for delimiting species, results in a different panorama of what should be protected. Our analysis shows that the current official Mexican endangered species list, BSC based, encompasses 371 birds, ranked as 277 species and 94 subspecies. The same list of protected forms changes under the phylogenetic species concept because 47 of them are not recognized as valid species, while another 28 forms merit higher levels of protection. Additionally, under this concept another 11 forms should be candidates for inclusion based on their restricted distribution. We call attention to the fact that the use of one or another species concept affects endangered species lists.