The effect of isolation and the importance of dispersal in establishing and maintaining populations in fragments of remnant habitat remain poorly understood. Nevertheless, environmental connectivity is likely to be important for ensuring the long-term preservation of biodiversity in extensively cleared landscapes. In this study, we compared reptile communities in large conservation parks with those in small woodland remnants 6.5–12 km from the parks, on the Eyre Peninsula, South Australia, Australia. We assessed the impact of fragmentation on the abundance, richness and habitat preferences of reptiles, and examined whether connection to linear roadside vegetation altered reptile communities in small woodland remnants. Of the 31 reptile species, 12 were restricted to conservation parks and six to habitat fragments in farmland. There was a substantial reduction in reptile species richness and abundance in farmland fragments. Direct connection of remnant vegetation to roadside corridors did not affect abundance of common species in the farmland fragments, although species richness was lower in isolated remnants in one of our two study regions. The habitat preference of the scincid lizard Menetia greyii differed between farmland fragments, where they were regularly found on dunes and roadsides, and conservation parks, where they were rare and not detected on dunes. We suggest that habitat fragmentation may have altered interspecific interactions, enabling an expansion of habitat use in the farming landscape. Significantly lower abundance of four common species in farmland settings compared with reserves indicated that existing corridors and small fragments provide inadequate connectivity over larger distances. To counter this effect, large reserves may need to be less than 10 km apart.