The intraspecific variation of mitochondrial cytochrome b sequence was analysed for two widely distributed Tunisian anuran species, Discoglossus pictus and Pelophylax saharicus. We observed low genetic variation within both species (D. p. auritus 0.6% uncorrected genetic distances, P. saharicus 0.2%) and the absence of genetic structure within both species in the studied region. There is no correspondence between previously described morphotypes of P. saharicus in Tunisia and our genetic data. Our results show a lack of phylogeographic structure in both species despite their fragmented distribution across Tunisia.