The Korean fir tree Abies koreana, an endangered species in Korea, faces threats primarily from climate change-induced stress and drought. This study proposed a sustainable method to enhance A. koreana drought tolerance using a black yeast-like fungus identified as Aureobasidium pullulans (AK10). The 16S/ITS metabarcoding analysis assessed the impact of drought and AK10 treatment on the seedlings' rhizosphere microbiome. Results revealed a profound drought influence on the microbiome, particularly affecting fungal mycobiota. Drought-stressed seedlings exhibited elevated Agaricaceae levels, opportunistic fungi generally associated with decomposition. AK10 treatment significantly mitigated this proliferation and increased the relative abundance of beneficial fungi like Cystofilobasidium and Mortierella, known biocontrol agents and phosphate solubilizers. A notable reduction in the phytopathogenic Fusarium levels was observed with AK10, alongside an increase in beneficial bacteria, including Azospirillum and Nitrospirillum. Furthermore, the conducted correlation analysis shed light on microbial interrelationships within the rhizosphere, elucidating potential co-associations and antagonisms. Taken together, the isolated A. pullulans AK10 identified in this study serves as a potential biostimulant, enhancing the drought tolerance in A. koreana through beneficial alterations in the rhizosphere microbiome. This approach presents a promising strategy for the conservation of this endangered species.