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. The genus Algyroides Bibron and Bory de Saint-Vincent, 1833 includes four Mediter-ranean lizard species with a relictual distribu-tion in southern Spain, Corsica and Sardinia, and the western and southern Balkan Penin-sula. They share unique morphological fea-tures among lacertid lizards including very large dorsal body scales with oblique keels (Har-ris, Arnold and Thomas, 1999). However, re-cently a molecular study questioned their mono-phyletic origin (Pavlicev and Mayer, 2009). The Pygmy Algyroides, Algyroides fitzingeri (Wieg-mann, 1834) is endemic to Corsica and Sar-dinia where it is quite widespread (Delaugerre and Cheylan, 1992; Salvi and Bombi, 2010). It mostly inhabits Mediterranean-type shrubby vegetation as well as temperate forests, rocky habitats, and dry walls along rural areas. Lit-tle is known about the biology of this elusive species (Schneider, 1981; Capula and Luiselli,