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Background and Aims Agricultural products deriving from the same genotypic clone often have different physical and sensory properties that influence their overall quality and value. Microorganisms may play key roles throughout the production of many crops, affecting plant and fruit health and modifying plant materials to produce socially and economically important commodities. Following this idea, we investigated whether fungal diversity both prior to and during fermentation was correlated with the concentration of three volatile thiols important to Sauvignon Blanc aroma and flavour. Methods and Results We used molecular and metagenomics approaches to quantify yeast populations and GC/MS to quantify thiols and analysed these using random forest statistical approaches. The species of Saccharomyces yeasts present at the end of fermentation are significantly correlated with the concentration of 4‐mercapto‐4‐methylpentan‐2‐one, while several other fungal species present in the must, which are known to be associated with vine and fruit health, are also correlated with thiol concentration. Conclusions These data highlight the relationship between the presence of Saccharomyces uvarum and the production of 4‐mercapto‐4‐methylpentan‐2‐one, while some members of the fungal community correlate with thiol concentration generally. Thus, components of the fungal community may potentially affect the accumulation of odourless precursors in grape via pathogenic effects during fruit ripening, but further research is required to confirm such speculation. Significance of the Study This work emphasises the need for a better understanding of the interactions between microbial populations and agricultural products, and has implications for the management of fungal diversity and disease in these systems.