The European rabbit, Oryctolagus cuniculus, was introduced to Australia in 1859 and quickly became a significant vertebrate pest species in the country across a wide distribution. In arid and semi-arid environments, rabbit populations exist as metapopulations - undergoing frequent extinction recolonisation cycles. Previous studies identified population genetic structuring at the regional level between arid and semi-arid environments, and habitat heterogeneity was suggested as a possible causal factor. For the most part, rabbit behaviour has been overlooked as a factor that could contribute to explaining population genetic structure in arid and semi-arid environments. This study utilised a combination of genetic sampling techniques and a simulated territorial intrusion approach to observing wild rabbit behaviour in arid and semi-arid environments. The genetic component of the study compared population samples from each region using four polymorphic microsatellite loci. The behavioural component examined variation in the level of territoriality exhibited by three study populations in the arid region towards rabbits of known versus unknown origins (resident vs transgressor (simulating dispersal)). A difference was observed in population genetic structure determined from nuclear markers between arid and semi-arid regions, which supports findings of previous research using mitochondrial DNA data in the same area. Additionally, differences in aggressive response to known vs unknown rabbits were identified in parts of the arid region, which together with the effects of habitat heterogeneity and connectivity may explain the observed differences in population genetic structure. Knowledge of behavioural plasticity and its effect on relative dispersal success and population genetic structure may contribute to improved management and control of feral rabbit populations at the regional level within Australia; and may assist with conservation efforts in the species' natural range in Europe.