The winemaking industry faces unprecedented challenges due to climate change and market shifts, with profound commercial and socioeconomic repercussions. In response, non- yeasts have gained attention for their potential to both mitigate these challenges and enhance the complexity of winemaking. This study builds upon our previous cataloguing of 293 non- yeast species associated with winemaking environments by rigorously analysing 661 publicly available genomes. By employing a bioinformatics pipeline with stringent quality control checkpoints, we annotated and evaluated these genomes, culminating in a robust dataset of 530 non- proteomes, belonging to 134 species, accessible to the research community. Employing this dataset, we conducted a comparative phylogenomic analysis to decipher metabolic networks related to fermentation capacity and flavor/aroma modulation. Our functional annotation has uncovered distinctive metabolic traits of non- yeasts, elucidating their unique contributions to enology. Crucially, this work pioneers the identification of a non- 'fermentome', a specific set of six genes uniquely present in fermentative species and absent in non-fermentative ones, and an expanded set of 35 genes constituting the complete fermentome. Moreover, we delineated a 'flavorome' by examining 96 genes across 19 metabolic categories implicated in wine aroma and flavour enhancement. These discoveries provide valuable genomic insights, offering new avenues for innovative winemaking practices and research. : Franco-Duarte R, Fernandes T, Sousa MJ, Sampaio P, Rito T, Soares P (2025). Phylogenomics and functional annotation of 530 non- yeasts from winemaking environments reveals their fermentome and flavorome. : 1-17. doi: 10.3114/sim.2025.111.01.