<p>Habitat destruction is the most pervasive threat to global biodiversity, leading to widespread population declines and range reductions. Land clearing can leave small, isolated populations persisting in remnant habitat, where demographic factors may erode genomic diversity and diminish adaptive potential. We compared the genomic structure, diversity, inbreeding and effective population sizes of fragmented populations on farms to nearby populations in large, continuous tracts of vegetation (national park) for three terrestrial lizard species in south-eastern Australia. Due to the small spatial scale of the study, observed levels of genomic differentiation among sampling locations were typically very low (<i>F</i>_ST &lt; 0.1). The farm locality of one species, the painted dragon (<i>Ctenophorus pictus</i>), showed substantially more differentiation to national park localities (<i>F</i>_ST &gt; 0.05) than the national park localities showed to one another (<i>F</i>_ST &lt; 0.01), suggestive of genetic isolation due to the agricultural matrix. Genomic diversity and effective population sizes were lower in farm populations compared to national parks for two of the three species, the exception being shrubland morethia (<i>Morethia obscura</i>), where genomic diversity was similar across site types. Inbreeding coefficients were generally comparable between farm and national park populations. Our findings highlight the genetic consequences of land clearing including low population size, low genomic diversity and higher risk of inbreeding depression. Despite these challenges, habitat fragments can maintain high biodiversity value, which can be maximised by management initiatives such as translocations and establishing habitat corridors.</p>