The presence of fungi in the coral microbiome is increasingly recognized, yet their potential impact on the holobiont's health, particularly under stress conditions, remains underexplored. To address this gap, we isolated over 200 strains (predominantly Ascomycota) from the common scleractinian Red Sea coral, Stylophora pistillata. Using conidia from a rare (Stachybotrys chlorohalonata) and a common (Cladosporium halotolerans) fungal symbiont, we investigated their effects on coral fragments maintained at ambient (25°C) and elevated (33°C) sea temperatures. Inoculation with S. chlorohalonata resulted in significant tissue loss, across both water temperature treatments. Conversely, inoculation with C. halotolerans did not result in visible effects at ambient temperature, but mitigated tissue loss at elevated temperature. This protective effect was accompanied by reduced expression of stress-induced peroxiredoxin-6 and Rad51 host genes, yet not that of Hsp70. Additionally, potential algal symbiont photosynthetic efficiency was higher by over 25% in the elevated temperature treatment, concurrent with higher bacterial diversity, including a marked reduction (>
3-fold) in the proliferation of Vibrionaceae in the C. halotolerans-treated coral nubbins. These findings reveal the contrasting impacts of fungal symbionts on coral health, highlighting the dual roles of the mycobiome in influencing holobiont resilience under environmental stress.