Disturbed landscapes can provide habitat for a variety of species; however, for fauna, a strong understanding of their habitat affiliations is critical both to detect species and to develop management prescriptions to maintain their populations. We assessed habitat affiliations of common, uncommon and rare reptile species in a multiple-use landscape, the northern jarrah forest of south-western Australia. To identify predictors of reptile occurrence, we related reptile presence/absence, or relative abundance, to habitat, climatic and seasonal variables. Because the reptiles studied have cryptic behaviours and low numbers of detections, we used a combination of analyses including non-metric multi-dimensional scaling, occupancy and regression models. We identified specific habitat affiliations for the most common species and potential linkages with vegetation structure for most uncommon species. There were insufficient detections to determine habitat affiliations accurately for most rare species. Often species were detected too infrequently to determine specific habitat variables that influence occupancy and detection, and altering survey time and scale may increase detections so that habitat affiliations can be determined. However, in highly speciose landscapes, like our study area, we may not be able to wait until we have enough detections to define the habitat affiliations of all reptiles before we make management decisions. Therefore management activities that maintain habitat heterogeneity and complexity is likely to be the best strategy to conserve the most reptile species.