Fungal ITS amplicon sequencing data (Illumina NovaSeq, 2 x 150 bp) from leaf, stem and bark tissues of five Eucalyptus cinerea trees in an intensively managed commercial cut foliage plantation in Co. Dublin, sampled on one day in July 2024. Tissues were pooled by compartment within each tree, giving 15 samples (5 trees x 3 compartments). Tissues were not surface-sterilised, so the profiles combine epiphytic and endophytic fungi. After quality control and DADA2 denoising, 405 fungal ASVs were retained. Bark carried richer, more diverse and phylogenetically broader fungal communities than leaf and stem: bark was dominated by Diaporthe, Peniophora and Talaromyces, and leaf and stem by Vishniacozyma and Sporobolomyces. Both compartment (PERMANOVA R2 = 0.239) and tree identity (R2 = 0.451) significantly affected community composition. The dataset is a baseline description of the fungal microbiome of E. cinerea grown commercially under Irish conditions.
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