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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 …