The southern hairy-nosed wombat (Lasiorhinus latifrons) is a cryptic, primarily nocturnal marsupial, for which behavioral information is notably lacking. Animals that are difficult to observe can be identified and tracked by individual-specific genotypes obtained from remotely collected DNA sources; wombats are excellent candidates for such an approach because freshly plucked hair is easily captured at burrow entrances. Twice a year during 1999–2001, we employed an intensive remote hair-collection regime coupled with individual-resolution genetic analysis to sample a South Australian population in a 63.3-km² protected conservation reserve. Individuals were identified using 5 highly polymorphic microsatellite markers and further examined using another 10 markers to resolve ambiguities, enabling assessment of burrow- and space-use patterns. Analyses of rate of discovery of new individuals indicated that nearly all wombats inhabiting the study area were detected (102); there were >1,000 “capture” events, and 90% of individuals were detected multiple times. Surprisingly, a female sex bias existed despite females being the dispersing sex. Space use was conservative and likely a reflection of adaptations enabling energy conservation. Transits between the northern and southern sections of the study area were nearly nonexistent. No sex or consistent seasonal differences were found in burrow, warren, or space use, other than in interaction with other factors. However, a strong increase in activity and space use in September 2001 relative to other sampling periods may be attributed to activities associated with mating. The thoroughness and evenness of this study's sampling strategy was markedly effective for this species, as, with appropriate modification and optimization, it will likely be for other shy and cryptic organisms.