In island ecosystems, reptiles play diverse ecological roles as a result of niche broadening, which increases potential niche overlap between species. Ecological niche partitioning is a means of reducing direct competition between coexisting species and differences in habitat use among island gecko species have been suggested as a by-product of specialization to feeding on certain resources. Here, we examine modes and drivers of niche partitioning of two endemic species of Phelsuma gecko (Phelsuma sundbergi and Phelsuma astriata) in relict native palm forest in the Seychelles to further understanding of congeneric reptile co-existence in native habitats. Phelsuma abundance, microhabitat use and habitat composition were quantified in different macrohabitat types. P. sundbergi showed a clear preference for habitat dominated by the coco de mer palm, Lodoicea maldivica and a strong association with male individuals of this dioecious species. P. astriata density increased significantly with arboreal biodiversity but did not display a relationship with a specific tree type. High levels of resource segregation were determined along the microhabitat axis, based on differential tree preference. Our results suggest that P. sundbergi and P. astriata may have evolved to co-exist in this habitat type through partitioning of microhabitat as members of a divergent specialist/generalist assemblage determined by consumption of L. maldivica pollen by P. sundbergi. Our findings concur with the hypothesis that differences in habitat use among island reptiles are a by-product of trophic specialization and support the conservation of native habitat for maintenance of reptile diversity.