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The phylogenetic affinities of Acanthodactylus beershebensis, a highly endangered lacertid lizard endemic to the Neguev (Israel), were assessed using mtDNA markers. Fragments of 12S and 16S rRNA were analysed and compared with already published sequences of Acanthodactylus. Results corroborate the taxonomic placement of A. beershebensis as a member of the A. pardalis group but place it within a polytomy at the same phylogenetic level as other (unnamed) African populations. This pattern of high but poorly structured genetic diversity, previously observed for other Acanthodactylus complexes, has been suggested to derive from the climatic instability of North Africa and the Middle East during the humid and dry periods of the Pleistocene as well as dune migrations. In conservation terms, if A. beershebensis is to be prioritised, then other populations of the A. pardalis group inhabiting North Africa would deserve a similar status, making their species definition urgent. These results highlight the need for considering phylogeny when establishing conservation priorities.