Populations occupying different microhabitats can either exhibit generalized traits across habitats or show intra-specific variability, adapting to each microhabitat to maximize performance. Intraspecific variability is important for studying evolutionary mechanisms promoting diversity and adaptation. Despite its importance, intra-specific variability is relatively little studied compared to variation between species occupying different habitats and microhabitats. We investigated whether populations of the gecko Mediodactylus kotschyi, that differ in the substrates they occupy, display microhabitat specific behaviour and functional morphology. We collected geckos from seven populations in Greece, under or on rocks or on trees. We tested their microhabitat preference and clinging ability in the lab. We measured the limb, digit, and claw morphometrics of geckos and examined their relationship to clinging ability. Geckos showed no preference to either substrate, regardless of the substrate on which they were found, or the availability of trees in their natural habitat. All geckos clang better to the tree, but the same claw morphology: shorter and higher claws, was associated with better clinging to both substrates. Our results suggest that although M. kotschyi cling better to trees than to rocks, their morphology enables them to occupy both substrates, a fact that may have aided them to inhabit the smallest, treeless islets in the Aegean Sea.