The phytopathogenic fungus, Fusarium oxysporum f. sp. koae, is recognized as the cause of wilt of Acacia confusa seedlings and trees in Taiwan. This study investigated the soil microbiome in an acacia plantation to assess its influence on the health of A. confusa. The health of plants is thought to be strongly correlated with soil microbial communities, and F. oxysporum is an important soil-borne pathogen. This study analyzed the microbial composition of the rhizosphere soil of both healthy and wilted acacia trees. Rhizosphere soils of healthy and wilted A. confusa in the acacia plantation were collected, and then DNA was extracted and sequenced using next-generation sequencing (NGS) to acquire sequences of the fungal internal transcribed spacer (ITS) and the bacterial 16S ribosomal DNA (16S rDNA). Results revealed no significant differences in the fungal or bacterial compositions at the class and genus levels between the soil microbiomes of healthy and wilted trees. Notably, Fusarium spp. was not a dominant fungal genus in either sample. Despite the higher microbial diversity observed in healthy trees compared to wilted ones, the difference was not statistically significant. A linear discriminant analysis (LDA) revealed several dominant microorganisms in the soil of wilted trees. These included the fungal genus Cephalotrichum, the bacterial phyla Gammaproteobacteria and Proteobacteria, the bacterial order Rhodanobacteraceae, and the bacterial families Kapabacteriales, Diplorickettsiales, and Xanthomonadales. Additionally, the bacterial genera, Lacunisphaera and Chujaibacter, were found to be prominent in the soil samples of wilted trees. This study represents the first analysis of the soil microbiome in an acacia plantation, shedding light on potential biological factors related to A. confusa wilt which may guide future research on microbiome-plant interactions.