Phytophthora cinnamomi, the oomycete responsible for Phytophthora Root Rot (PRR), poses a critical threat to global avocado production. While phosphite fungicides effectively manage PRR, prolonged use risks the development of resistance. The rhizosphere—a dynamic interface between plant roots and soil microorganisms—harbours diverse and potentially beneficial microbial communities. Understanding these communities in the presence or absence of Phytophthora could identify microbial consortia for disease suppression. This study characterised the rhizosphere microbiome of orchard-grown Reed avocados in Western Australia using 16S and ITS amplicon sequencing. Soil samples were collected from thirteen orchards, where Phytophthora was detected in seven (Phytophthora-positive) and absent in six (Phytophthora-negative). Indicator species analysis identified microbial taxa consistently associated with Phytophthora-positive and -negative samples. 405 bacteria taxa (e.g., Vicinamibacterales, Rhizobiales) were associated with Phytophthora-negative samples, while 308 bacteria taxa (e.g., Pedosphaeraceae, Solirubrobacterales) were linked to Phytophthora-positive samples. Differential fungal taxa identified include 150 in Phytophthora-negative samples (e.g., Cladosporium herbarum, Talaromyces spp.) and 86 taxa in Phytophthora-positive samples (e.g., Saitozyma podzolica, Fusarium oxysporum). These findings suggest that a microbiome community associated with Phytophthora-negative samples may play an important role in PRR, offering insights into sustainable avocado disease management strategies.