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The invasive soilborne plant pathogen Phytophthora cinnamomi Rands is a major threatening process in the South-west Botanical Province of Western Australia, an internationally recognised biodiversity hotspot. Comparatively recent introduction of P. cinnamomi into native plant communities of the South-west Botanical Province of Western Australia since the early 1900s has caused great irreversible damage and altered successional change to a wide range of unique, diverse and mainly susceptible plant communities. The cost of P. cinnamomi infestation to community values is illustrated by examination of direct (mortality curves, changes in vegetation cover) and indirect impacts on biodiversity and ecosystem dynamics, the proportion of Threatened Ecological Communities infested, Declared Rare Flora either directly or indirectly threatened by infestation and estimates of the proportion of the native flora of the South-west Botanical Province susceptible to the pathogen. While direct impacts of P. cinnamomi have been poorly documented in the South-west Botanical Province, even less attention has been given to indirect impact where destruction of the habitat by the pathogen affects taxa not directly affected by infection. Current poor understanding and quantification of indirect impacts of P. cinnamomi through habitat destruction results in an underestimation of the true impact of the pathogen on the flora of the South-west Botanical Province. Considerable variation of susceptibility to P. cinnamomi among and within families of threatened flora and responses of taxa within the genus Lambertia show how classification within family and genus are poor predictors of species susceptibility. Within apparently susceptible plant species, individuals are resistant to P. cinnamomi infection. Intra-specific variation in susceptibility can be utilised in the long-term management of threatened flora populations and needs to be a high research priority. Current control strategies for conservation of flora threatened by P. cinnamomi integrate hygiene and ex situ conservation with disease control using fungicide. Application of the fungicide phosphite has proven effective in slowing progress of P. cinnamomi in infested, threatened communities. However, variation in plant species responses to phosphite application is a major factor influencing effective control of P. cinnamomi in native communities. A greater understanding of the mechanisms of action of phosphite in plant species showing different responses to the fungicide may provide options for prescription modification to increase phosphite effectiveness in a range of plant species. The range of responses to P. cinnamomi infection and phosphite application described for Lambertia taxa suggests that the genus would make an ideal model system to elucidate the mechanisms of resistance to P. cinnamomi and the effectiveness of phosphite against the pathogen.