The issues that influence the application of the fungicide phosphite (phosphonate) to natural plant communities affected by Phytophthora cinnamomi Rands are complex. Research has shown significant protective effects that are valued in the preservation of rare and endangered plant species and communities. However, phosphite does have other effects that include phytotoxicity, growth abnormalities, reduced reproductive capacity and large difference in levels of P. cinnamomi control between plant species. Clearly a balanced approach needs to be adopted when using phosphite for the management of P. cinnamomi in natural ecosystems. It is necessary to take into account the beneficial and detrimental effects of phosphite and the possible loss of plant species if the fungicide is not used. Traditional forms of P. cinnamomi management are also outlined to highlight their continued importance in disease management, irrespective of whether phosphite is used or not.