Hardenbergia mosaic virus (HarMV), genus Potyvirus, belongs to the bean common mosaic virus (BCMV) potyvirus lineage found only in Australia. The original host of HarMV, Hardenbergia comptoniana, family Fabaceae, is indigenous to the South-West Australian Floristic Region (SWAFR), where Lupinus spp. are grown as introduced grain legume crops, and exist as naturalised weeds. Two plants of H. comptoniana and one of Lupinus cosentinii, each with mosaic and leaf deformation symptoms, were sampled from a small patch of disturbed vegetation at an ancient ecosystem-recent agroecosystem interface. Potyvirus infection was detected in all three samples by ELISA and RT-PCR. After sequencing on an Illumina HiSeq 2000, three complete and two nearly complete HarMV genomes from H. comptoniana and one complete HarMV genome from L. cosentinii were obtained. Phylogenetic analysis which compared (i) the four new complete genomes with the three HarMV genomes on Genbank (two of which were identical), and (ii) coat protein (CP) genes from the six new genomes with the 38 HarMV CP sequences already on Genbank, revealed that three of the complete and one of the nearly complete new genomes were in HarMV clade I, one of the complete genomes in clade V and one nearly complete genome in clade VI. The complete HarMV genome from L. cosentinii differed by only eight nucleotides from one of the HarMV clade I genomes from a nearby H. comptoniana plant, with only one of these nucleotide changes being non-synonymous. Pairwise comparison between all the complete HarMV genomes revealed nucleotide identities ranging between 82.2% and 100%. Recombination analysis revealed evidence of two recombination events amongst the six complete genomes. This study provides the first report of HarMV naturally infecting L. cosentinii and the first example for the SWAFR of virus emergence from a native plant species to invade an introduced plant species. © 2014.