Algyroides fitzingeri is a Corso-Sardinian endemic lizard belonging to a relictual genus within the Lacertini radiation. In recent phylogeographic studies of Corso-Sardinian endemic lizards incongruent patterns are emerging. We investigated the mitochondrial genetic variation of A. fitzingeri across Corsica and Sardinia to obtain a preliminary portrait of its phylogeographic history. This species showed some polymorphism, but with low genetic differentiation between populations, that probably originated during the Pleistocene. Corsican populations are closely related to those from North Sardinia and are likely to have originated from them, given the higher diversity and deeper phylogeographic structure observed in Sardinia than in Corsica. While the phylogeographic structure of A. fitzingeri in Corsica is surprisingly shallow when compared with other co-distributed lizards, in Sardinia a common pattern apparently emerges. Further research is needed to confirm the hypotheses here presented and to provide a conclusive assessment of the phylogeography of this species.