Three Meriones species inhabit Tunisia, namely M. shawi, M. libycus and M. crassus, but little genetic data exist on these gerbils. We collected Meriones from eight localities in Tunisia, and obtained mitochondrial (cytochrome b) and nuclear (IRBP) gene sequence data for 37 and 13 specimens, respectively, belonging to two species: M. shawi and M. libycus. We also optimised three microsatellite markers previously described in M. unguiculatus to obtain a finer analysis of their genetic diversity and geographic structure, given their wide distribution. Phylogenetic inferences of cyt b and IRBP data for these species, in the context of other gerbillin data, corroborate their taxonomic affinities reported by previous studies. High cyt b haplotype diversity was observed in both species (25 haplotypes in 29 and 27 sequences for M. shawi and M. libycus, respectively) with little geographical structure for M. shawi but three divergent groups in M. libycus. The average microsatellite diversity within each population was high (HO ≥ 0.6, HE ≥ 0.8) with M. libycus populations attaining the highest values. Population differentiation was moderate for several population pairs (Fst ≥ 0.1), the highest being between M. shawi populations. However, genetic distance among populations was not significantly correlated with geographic distance in either M. shawi or M. libycus. Our results contribute to a better characterisation of Tunisian Meriones species, suggesting high geographic structure in mtDNA of M. libycus populations within North Africa.