The prevalence of koala retrovirus (KoRV) provirus (DNA) and the average number of proviral insertions per cell vary in different free-ranging koala (Phascolarctos cinereus) populations across Australia. Populations in the northern states of Queensland and New South Wales have 100% proviral prevalence and mean proviral copy number of 140–165 per cell. In contrast, the proviral prevalence in the southern states of Victoria and South Australia differs among populations, with a mean prevalence in these states’ mainland populations of 73% and 38%, respectively and with the prevalence on southern island populations ranging from 0–50%. The proviral load in southern populations is comparatively low, with some populations having an average of less than 1 proviral copy per cell. The KoRV RNA load in plasma shows a similar discordance between northern and southern populations, with consistently high loads in northern koalas (103 to 1010 RNA copies per ml plasma), and loads ranging from 0 to 102 copies per ml in southern KoRV provirus-positive koalas. The variation in KoRV proviral prevalence and the disparity in proviral and viral loads between northern and southern koalas may reflect different types of infection in the two populations (endogenous versus exogenous). Alternatively, it is possible that KoRV has been present for a longer time period in northern populations resulting in differences in the host-virus relationship.