Previous phylogeographic studies based on mitochondrial DNA (mtDNA) markers have revealed a complex evolutionary history for the Italian wall lizard, Podarcis siculus, characterized by a geographically structured diversity of lineages. These lineages were shaped by allopatric divergence within multiple southern refugia, likely during the Pleistocene. In this study, a total of 294 Podarcis siculus specimens from 121 localities were genetically analyzed using microsatellite markers to: (i) assess whether the genetic substructure detected in mtDNA is reflected in nuclear microsatellite markers, (ii) evaluate potential cases of mito-nuclear discordance, and (iii) determine the extent of admixture resulting from gene flow between mtDNA haplogroups. The analysis identified eight genetic clusters, whose spatial distribution partially aligns with the mitochondrial structure. However, several discrepancies were observed, primarily in Southern Italy and Sicily. These include differences in the location of the contact zone between the two main lineages and the absence of genetic structure in some regions (e.g., Sicily), despite the presence of multiple parapatric mtDNA lineages. Possible explanations for mito-nuclear discordance involve a combination of factors, including the different evolutionary timescales captured by mitochondrial DNA and microsatellites, differential introgression of nuclear versus mitochondrial genes, and distinct dispersal patterns, potentially influenced by sex-biased philopatry, which affect gene flow among populations.