Deciphering the process of genetic differentiation of species with insular distributions is relevant for biogeographic and conservation reasons. Despite its importance as old gondwanic islands and part of the Western Indian Ocean biodiversity hotspot, little is known concerning the genetic structure of taxa from the Seychelles islands. We have examined patterns of structure and isolation within Urocotyledon inexpectata (Reptilia: Geckkonidae), an endemic species from this archipelago. Genetic diversity was screened from populations across the archipelago for both mitochondrial and nuclear genes. Gene genealogies and model-based inference were used to explore patterns and timings of isolation between the main lineages. High levels of genetic diversity were found for the mitochondrial and some of the nuclear markers. This species harbours at least two highly differentiated lineages, exclusively distributed across the northern and southern groups of islands. The main split between these was dated back to the Miocene/Late Pliocene, but isolation events throughout the Pliocene and Pleistocene were also inferred. Migration between groups of islands was apparently non-existent, except for one case. The low dispersal capabilities of this species, together with the intrinsic fragmented nature of its geographic distribution seem to have resulted into highly structured populations, despite the cyclic periods of contact between the different island groups. These populations may currently represent more than one species, making U. inexpectata another example of morphologically cryptic lineages with deep genetic divergence within gekkonids. The observed patterns suggest a hypothetical biogeographic scenario (of a main north – south phylogeographic break) for the Seychelles that can be further tested with the exploration of the phylogeographic structure of other Seychellois taxa.