The water frog Pelophylax saharicus is the most widespread anuran in North Africa and thus subjected to widely differing environmental conditions in different parts of its distribution range. In this paper we examined genetic structure of species 15 populations across Tunisia and eastern Algeria. We evaluated a potential role of mountain ranges as significant barriers to gene flow, using a partial sequences of the mitochondrial cytochrome oxidase I gene (COI). Twenty haplotypes were recorded in a total sample of 38 individuals, whereas, an overall low genetic variation of 0.4% was observed. AMOVA revealed no significant genetic structuring related to the 4 groups across the studied area. Unimodal mismatch distributions and significantly negative values of Fu's Fs and Tajima's D statistics support a recent expansion of populations from a smaller founder population as the most plausible explanation of the observed significant deviations from neutrality in the North-East African green frog populations.