We applied genetic tagging (the identification of individuals by genetic markers) as part of a demographic and genetic analysis of a manipulative study of bush rats Rattus fuscipes in a fragmented landscape in south-eastern Australia. Our study comprised bush rat populations from 30 remnant patches embedded within an extensive exotic pine plantation. Genetic tagging was applied at 12 sites where eight or more animals were encountered in the initial census. Out of a total of 701 DNA samples, we determined (by genetic analysis at 11 microsatellite loci) that 588 bush rat individuals were sampled. Genetic tagging proved to be highly effective, with 97% of animals uniquely identified with three loci, and all animals identified by six loci. Mark–recapture distances moved by genetically tagged animals from the control sites and post-perturbation treatment samples were highly restricted, with a mean of 35 m (35.3±4.5, mean±se, max. 280 m, n=109). This mean distance moved appears to be lower than for other comparable studies of the species. Fragmentation and above-average densities of animals may partially explain this result. An analysis of the factors affecting mark–recapture distance indicated that there was a significant effect of trap layout on the maximum movement detected, but no significant difference in mark–recapture distance between the sexes. We have demonstrated that genetic tagging can facilitate traditional capture–mark–recapture studies in bush rats and pave the way for subsequent population genetic analyses that can offer additional insights not available from ecology alone.