Approximately 90% of native vegetation has been cleared for agriculture in central New South Wales, Australia. Habitat loss has reduced and fragmented populations of the agamid lizard Amphibolurus nobbi. We compared genetic structure of populations of this species in an unmodified landscape with those from small nature reserves and linear remnants in farming areas. We ask: Is there evidence for reduced dispersal and population fragmentation among farm populations? Using 2008 bp mtDNA sequences and allozyme electrophoresis, we found that small populations in farming areas had as much genetic variation as populations in nature reserves. Application of nested clade analysis (NCA) indicated isolation-by-distance effects among populations from uncleared areas, but not among populations within farming locations. The genetic evidence therefore implied a high level of migration in the cleared landscapes. High dispersal after fragmentation may have resulted from either a burst of movement at the time of land clearing with dragons from many sources finding refuge in a few remnants, or from ongoing rapid dispersal through unsuitable habitat. A phylogeny based on mtDNA revealed that A. nobbi populations in the study area are deeply divided into two reciprocally monophyletic groups. Although we did not sample the entire species range, one of these evolutionarily significant units was only detected in remnant vegetation in the agricultural landscape. Therefore, a substantial subclade of this species may be vulnerable to extinction. Our findings emphasize that local populations of widespread species can harbour important intraspecific genetic diversity, supporting the case for maintaining widespread species throughout production landscapes.