Abstract We investigated the effect of forest fragmentation on the abundance of the gekkonid lizards Coleodactylus amazonicus and Gonatodes humeralis in fragments associated with Amazonian savanna near Alter do Chão, Pará, Brazil. These fragments have been isolated for at least 150 years and probably more. Abundance of lizards, tree density and food availability were estimated in 1000-m transects in eight sites in continuous forest and 21 forest fragments, ranging in size from 3.6 to 360 ha and distant from ∼150–10 000 m from continuous forests. Coleodactylus amazonicus was at least an order of magnitude more adundant than G. humeralis in continuous forest, and both species were negatively affected by fragmentation. Coleodactylus amazonicus was encountered only in continuous forest, the largest fragment, and one fragment adjacent to continuous forest. Gonatodes humeralis occurred in the majority of fragments, but was more common in continuous forest, and occurred in lower densities in fragments more distant from continous forest. The species with lowest recorded densities in continuous forest was the most resistant to fragmentation, contrary to what would be predicted from neutral models, such as island-biogeography theory, possibly because other factors are more important than initial population size in long-term fragmented landscapes.