Context. Habitat loss and fragmentation are leading causes of biodiversity decline worldwide. In Australia, woodland habitat has been extensively cleared and fragmented yet there has been limited research on the effects of habitat loss and fragmentation on semi-arid reptiles, impeding conservation planning and recovery efforts.

Aims. We aimed to investigate factors influencing the distribution and occurrence of habitat specialist and generalist reptile species on a large agricultural holding in south-eastern Australia that has experienced habitat loss and fragmentation.

Methods. Reptiles were surveyed using pitfall and funnel traps and active searches across 20 sites stratified by land use and vegetation type. Twelve sites were established in remnant woodland patches embedded within an agricultural matrix and eight sites were established in a private conservation reserve on the same property. Generalised linear models were used to explore relationships between the occurrence of eight reptile species and predictor variables describing site, landscape and vegetation variables.

Key results. Of the 31 reptile species that were detected, eight were modelled. The results revealed that four specialist species, the eastern mallee dragon (Ctenophorus spinodomus), nobbi dragon (Diporiphora nobbi), barred wedge-snouted ctenotus (Ctenotus schomburgkii) and shrubland pale-flecked morethia (Morethia obscura), were closely associated with the conservation reserve, and that the southern spinifex ctenotus (Ctenotus atlas) had a strong association with spinifex (Triodia scariosa) dominated vegetation community.

Conclusions. Reptile habitat specialists are particularly sensitive to habitat loss and fragmentation and are at a higher risk of local extinction compared with habitat generalists. Reptile occurrence was reduced in remnant woodland patches, but remnant patches also supported a suite of habitat generalists.

Implications. A suite of semi-arid reptile species are sensitive to the effects of habitat loss and fragmentation and are susceptible to localised extinction. However, the presence of habitat generalists within woodland remnants highlights the value of retaining representative habitat patches in agricultural landscapes. Conservation of semi-arid woodland reptiles will depend on the retention of large tracts of protected vegetation across a broad range of soil types to maintain habitat heterogeneity and reptile diversity.