We collected field data to characterize and segregate the microhabitat use of the three sympatric bent-toed geckos Cyrtodactylus phongnhakebangensis, C. cryptus, and C. roesleri. These species were recently discovered to occur in one of the last remaining karstic rainforest formations in Vietnam, the Phong Nha-Ke Bang National Park of Central Vietnam. Between July and September 2010, we found 126 individual geckos in six independent areas by visual encounter surveys. We assessed habitat data in order to enable a microsite comparison of the different species. We found syntopic occupation of one study site by C. phongnhakebangensis and C. roesleri, and sympatric occurrence with C. cryptus. Our study shows niche segregation in microsite use for C. cryptus and niche overlap for C. roesleri with C. phongnhakebangensis. It may be inferred that the syntopic sibling species did not develop microhabitat partitioning, while the sympatric gecko adjusted to occupy different types of habitat.