In this study we address the genetic and morphological variability of the Balearic lizard. We updated the phylogeny of the current populations of Podarcis lilfordi incorporating new molecular markers. Our results indicate a lack of agreement between genetic and morphological diversification. We do not find a congruent relationship between both data sets and the current subspecific arrangement. From our viewpoint, the solution does not imply a traditional subspecific review. Such review would lead us to either the recognition of a very large number of subspecies with little or no support on genetic data, or a massive grouping of populations in a very small number of subspecies that would mask their diversity. As a solution to this dilemma, we propose a paradigm shift with the recognition of evolutionarily significant units (ESU) for each of the current populations of the Balearic lizard. The recognition of ESUs implies that each and every one of the populations of the Balearic lizard must be preserved if we want not only to preserve the extraordinary current biodiversity, but to preserve indefinitely the evolutionary process that has given rise to it and that can only be guaranteed if we maintain all the environmental scenarios in which that evolution has been verified.