AbstractThe Wall Gecko shows heterogeneous colour pattern, which may vary among individuals, depending on the time of day and on the habitat segregation. Nocturnal pale geckos live exclusively on walls. Diurnal dark geckos preferentially live on olive tree trunks, demonstrating an ability to change skin colour that is superior to that of the pale gecko and allows diurnal geckos becoming camouflaged on the diverse substrates occupied during the day. In our study, the nocturnal/pale/wall and diurnal/dark/trunk geckos could be considered the extremes of an ecological cline of morphological variation on which divergent selection may be acting. Combining the effect of balancing selection on nocturnal geckos and disruptive selection between two sympatric populations could lead to speciation. All geckos analysed here belong to the same species, as confirmed by genetic characterization, however diurnal and nocturnal gecko populations seem to be in an early stage of incipient speciation. These two different morphs still combine genes, as revealed by neutral genetic markers, yet they show complete separation according to the analyses of mtDNA coding genes. Experimental results show that diurnal and nocturnal geckos do not swap their niches, likely because the predation pressure causes severe selection for background matching. Genomic analysis of complete mtDNA suggests that nocturnal geckos seem to be under balancing selection perhaps due to the narrow niche in which they live, whereas the daytime population has more opportunity in fitting into the multiple available niches, and they experience positive selection. Here we hypothesize that the ecological segregation that we are witnessing between the nocturnal and diurnal geckos, can lead to a ecological speciation.