The land snail Solatopupa guidoni has an interesting disjunct distribution in the peri-Tyrrhenian area, with a few scattered populations in Sardinia, Corsica, and Elba Island. The species is strictly bound to limestone and has poor dispersal capacity. Here, we used sequences of two mitochondrial genes, cytochrome oxidase I (COI) and 16S rRNA (16S), to reconstruct the species phylogeography. The study is based on nine of the 13 populations reported in the literature. Phylogenetic methods and nested clade analysis failed to retrieve reciprocally monophyletic lineages on each island. Sardinian and Elba Island populations were found to be embedded within those of Corsica. These results contrast with previous phylogeographic studies of other organisms with similar distribution patterns, showing major phylogeographic breaks between islands. Molecular clock estimates suggest that species diversification occurred less than 2.5 Myr ago, in line with a previous study that dated the split of S. guidoni from its continental sister species at 3–5 Myr. Corsican populations can be tentatively sorted into two haplo-groups. A first group includes haplotypes found in central inland Corsica only, whereas haplotypes found in northern coastal locations cluster in a second haplo-group. The latter also includes Sardinian and Elba Island populations. Molecular data indicate that a combination of vicariance and dispersal events provide the best explanation of the distribution of this species.