Identifying the characteristics that make a species vulnerable to extinction following habitat fragmentation is one of the most pressing problems in conservation biology. One suggestion is that habitat specialists are less able to cope with rapid changes to their habitat or to move through the modified landscape than habitat generalists and so will be more vulnerable to extinction. We examine this hypothesis by comparing the distribution of two species of gecko, Gehyra variegata and Oedura reticulata, in patches of remnant woodland. The former species is a habitat generalist relative to the latter and shows a markedly higher level of persistence (97% remnant occupancy vs 72%). Logistic regression modelling of the presence or absence of O. reticulata revealed a significant correlation between the number of smooth-barked eucalypts (both species preferred by O. reticulata) in the remnant and the presence of O. reticulata. This suggests that the probability of extinction for a given population is related to the amount of suitable habitat in the remnant and is a function of processes operating at the population level rather than on a regional basis. Pitfall trapping in this study and evidence from another long-term study suggest that the movement of O. reticulata between remnants is negligible. As a consequence, this species has been unable to form a metapopulation at equilibrium. In contrast, it is likely that G. variegata is maintaining its widespread distribution through a metapopulation structure. These results demonstrate the importance of the ability to form a metapopulation for a species to maintain persistence in recently and highly fragmented ecosystems.