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In this work, a total of 72 commercial table olive packages obtained from different international markets were analysed to determine their fungal biodiversity. Viable fungal counts ranged from the detection threshold (<1.6 log 10 CFU/g in 25% of cases) to a maximum of 5.86 log 10 CFU/g. Assignation of fungal taxonomy was carried out through a metataxonomic analysis of the ITS region, which revealed that almost half of the total sequences obtained from all packages corresponded to the Pichia genus (44.08%), followed by Citeromyces (14.45%), Candida (8.07%), and Wickerhamomyces (6.95%). In lower proportions were also detected other genera such as Starmerella (3.60%), Saccharomyces (2.24%), Debaryomyces (2.08%), and Dekkera (2.05%). The statistical analysis allowed to link certain taxa to specific types of elaboration (lye treated, green, and black natural olives), presentation (pitted, whole, or sliced samples), and packaging material/system (glass, PET, plastic bags, and vacuum). Likewise, Zygotorulaspora genus was especially sensitive to the presence of potassium sorbate, while other genera such as Sporobolomyces , Moniliella , and Gibellulopsis were more abundant in packages treated with this preservative. Lastly, potential pathogenic fungal genera such as Alternaria, Kodamaea, Lodderomyces, Malasessia, or Aspergillus were detected in low proportions (<0.3%), although with higher representation in some individual samples. Our results contribute to improving our knowledge of the fungal population associated with this ready-to-eat fermented vegetable, providing us a strong tool to assess the safety, stability, and quality of the final product. • Metataxonomic approach of ITS region was applied in global commercial olive packages. • Half of total sequences obtained from all packages corresponded to the Pichia genus. • Potential pathogenic fungi were detected in high representation in some samples. • The presence of certain fungal taxa was influenced by the packaging conditions. [ABSTRACT FROM AUTHOR]