The ocellated lizards in the Timon lepidus/tangitanus/pater complex include the largest lacertids living in continental Europe and North Africa. Long considered a single species (T. pater), the division of the North African ocellated lizards into two species, T. pater in Tunisia and Algeria, and T. tangitanus in Morocco, is now accepted. In this study we investigated the patterns of genetic diversity in T. tangitanus and T. pater across North Africa. We analysed 12s rRNA and 16s r RNA mtDNA fragments of 26 new samples plus 19 sequences from previous studies, using parsimony, likelihood and Bayesian approaches. Our results confirm the two North African species as well-defined entities. Within T. tangitanus from Morocco, three genetically divergent lineages with geographic congruence were uncovered; one in the north, another widely spread across Central Morocco and one in the High Atlas and farther south. A high level of divergence among the Moroccan lineages suggests the split occurred just after the divergence between T. tangitanus and T. pater. Similar patterns have been found in other species, although more studies are needed to understand the biogeographical events shaping the complex diversity in this region.