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Here, we compared the gut mycobiota of 67 COVID-19 patients, 35 H1N1-infected patients and 48 healthy controls (HCs) using internal transcribed spacer (ITS) 3-ITS4 sequencing and analysed their associations with clinical features and the bacterial microbiota. Compared to HCs, the fungal burden was higher. Fungal mycobiota dysbiosis in both COVID-19 and H1N1-infected patients was mainly characterized by the depletion of fungi such as <jats:italic>Aspergillus<\/jats:italic> and <jats:italic>Penicillium<\/jats:italic>, but several fungi, including <jats:italic>Candida glabrata<\/jats:italic>, were enriched in H1N1-infected patients. The gut mycobiota profiles in COVID-19 patients with mild and severe symptoms were similar. Hospitalization had no apparent additional effects. In COVID-19 patients, Mucoromycota was positively correlated with <jats:italic>Fusicatenibacter<\/jats:italic>, <jats:italic>Aspergillus niger<\/jats:italic> was positively correlated with diarrhoea, and <jats:italic>Penicillium citrinum<\/jats:italic> was negatively correlated with C-reactive protein (CRP). In H1N1-infected patients, <jats:italic>Aspergillus penicilloides<\/jats:italic> was positively correlated with Lachnospiraceae members, <jats:italic>Aspergillus<\/jats:italic> was positively correlated with CRP, and Mucoromycota was negatively correlated with procalcitonin. 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