The southwest Australian floristic region (SWAFR) is an internationally recognized 'hot spot' of global biodiversity and has an endangered flora. It represents a unique interface between an ancient ecosystem and a recent agroecosystem, providing the opportunity to investigate encounters where the recipient of the virus is an introduced crop and the donor a native plant and vice versa. Phylogenetic analysis of the virus coat-protein genes was used to study isolates of three potyviruses representing different 'new encounter' scenarios at this interface. The incidence, symptomatology, host range, non-persistent aphid transmission and considerable genetic diversity of the first indigenous virus described from the SWAFR, where it infects the native legume Hardenbergia comptoniana, and its potential to damage lupin, a locally important, newly introduced cultivated grain legume, was studied. The name Hardenbergia mosaic virus is proposed for this virus. Two other examples of 'new encounter' scenarios involving other legume-infecting potyviruses studied were: Passion fruit woodiness virus, which has been found only in Australasia, where it damages recently introduced species of Passiflora and legumes; and Bean yellow mosaic virus, which is not indigenous to Australia and was introduced recently to the SWAFR, where it infects a number of introduced legumes, but also damages the local native legume Kennedia prostrata. Isolates of the former had considerable genetic diversity consistent with the virus being indigenous, while isolates of the latter virus from K. prostrata had a low genetic diversity consistent with recent arrival. This research illustrates how introduced viruses can damage indigenous plants and indigenous viruses can damage introduced cultivated plants within this unique ecosystem, and how human activities can facilitate damaging 'new encounters' between plants and viruses.