The growing recognition of the importance of microbial communities in shaping plant health and ecosystem function underscores the potential value of metagenomic analysis for plant conservation. We analyzed the bacterial diversity present in the leaves of ebony, a vulnerable species endemic to Sulawesi, Indonesia and one of the most expensive woods worldwide. The bacterial diversity was compared between symptomatic and asymptomatic leaves from two developmental categories, young plants (pole) and mature plants (tree). The microbial communities in asymptomatic and symptomatic leaves of D. celebica were analyzed using the 16S rRNA metagenomics to identify differences associated with the fitness of D. celebica. The results showed that the contributing factors to bacterial diversity in asymptomatic and symptomatic leaves were the plant’s developmental stage, environmental conditions, and the severity of pathogen attacks. Abundant bacteria at the phylum level across samples were Proteobacteria, Actinobacteria, and Firmicutes, whereas at the genus level were Sphingomonas, Jatrophihabitants, Bacillus, Methylobacterium, and Methylocella. At the genus level, a higher abundance of potentially beneficial bacteria was more evident in symptomatic leaves than their asymptomatic counterparts, specifically during the pole phase (young plant) than the tree phase (mature plant). This suggests that plants, particularly the young ones, activate defence mechanisms to ward off pathogen invasion by recruiting antipathogenic bacteria to fortify their less developed defence systems than mature plants. This research offers valuable insights into the potential roles of bacteria in D. celebica fitness.