Orchids are unique as they lack a functional rooting system and share an obligate relationship with their fungal symbionts. This relationship supports their host’s nutritional demands from seed germination to its later development. The orchid fungal endophytes explore large areas in the soil as, to which orchid roots have no access, and thus acquire both organic and inorganic nutrients beyond the depletion zone at low carbon cost. Both ‘autotrophic’ (green) and ‘mycoheterotrophic’ species occur in the Orchidaceae, but the term ‘mixotrophic’ is possibly a truer description of the carbon economy of many green orchids. Some of the major ecological threats of an Australian landscape are habitat destruction and fragmentation. There is little known about the nutritional sources and saprophytic ability of orchid mycorrhizal fungi (OMF) and their role in providing nutrition to orchids. However, several integrated approaches have been developed for the conservation, management and restoration of these plants in wild but there is an urgent need to set appropriate conservation priorities to prevent the loss of habitats for these endangered species in terms of their fungal endophytes. This chapter focuses on the protection of these endangered Australian orchid species by understanding the nutritional behavior of their endophytes.