Myrtle rust, caused by Austropuccinia psidii (formerly Puccinia psidii), is a significant invasive fungal pathogen that poses a serious threat to plants in the Myrtaceae family worldwide. Of the approximately 6,000 myrtle species globally, over 480 have been identified as susceptible, with the host range expanding due to the emergence of a highly virulent biotype. Since the detection of the pandemic biotype in New Zealand, this pathogen has rapidly spread, endangering iconic and ecologically significant myrtaceous flora. First reported in New Zealand in 2017, myrtle rust now affects over 19 native and 17 exotic Myrtaceae species. This study investigates fungal communities associated with myrtle rust infection and identifies potential mycoparasites for use as biocontrol agents. Symptomatic and asymptomatic leaves of native plants, ramarama (Lophomyrtus bullata) and pōhutukawa (Metrosideros excelsa), were collected from four regions across New Zealand (Taranaki, Rotorua, Auckland, and Christchurch). Metabarcoding was used to characterize the fungal microbiome. The results revealed a greater relative abundance of fungal taxa in asymptomatic leaves compared to symptomatic ones. Dominant genera in asymptomatic samples included Colletotrichum, Ilyonectria, Janinaea, Neopestalotiopsis. Pseudozyma, Ramularia, Simplicillium, Vishniacozyma and Zealoasperisporium. In contrast, symptomatic leaves were dominated by Ganoderma, Lophiotrema, Neosetophoma, Pucciniales and Septobasidium. A total of 205 fungal isolates (148 epiphytes and 57 endophytes) were recovered and identified, representing 64 genera. Of these, 18 putative mycoparasites from 9 genera (Alternaria, Cladosporium, Clonostachys, Epicoccum, Myrothecium, Paraconiothyrium, Phlebiopsis, Trichoderma and Sclerostagonospora) were selected for antagonistic activity screening against A. psidii. Three in vitro bioassays were conducted: a detached branchlet assay, spore germination test, and pathogenicity test. Two promising isolates from the genera Cladosporium and Trichoderma were identified, showing 33 -35% colonization of rust pustules two weeks after application and inhibiting 63 - 70% of rust uredospore germination, respectively. These isolates were considered as not pathogenic towards ramarama and pohutukawa with no disease symptoms developing on the inoculated leaves. These selected isolates were further tested under greenhouse conditions with three treatment approaches: putative mycoparasites alone, preventive application (two days before rust inoculation), and curative application (seven days after rust inoculation). Preventive treatments significantly reduced disease severity compared to curative applications. Metabarcoding analysis revealed that Trichoderma and Cladosporium persisted on leaves, comprising 4%, 2%, and less than 1% of the fungal community at 3, 9, and 21 days post-inoculation, respectively. Additionally, the Trichoderma isolate promoted plant regeneration, significantly increasing new shoot growth compared to Cladosporium and the control five weeks after treatment. The interactions between putative mycoparasites Cladosporium, Trichoderma and A. psidii were examined through scanning electron microscopy. These findings contribute to understanding the role of microbial communities in myrtle rust infection and inform the development of biocontrol strategies.