Critically ill COVID-19 patients requiring mechanical ventilation in the intensive care unit are at risk of developing invasive candidiasis. In this study we aimed to (1) characterize oral cultivable mycobiota of mechanically ventilated adult COVID-19 patients in an ICU setting by sampling four distinct oral niches in two fixed time points with regards to oral health status, (2) investigate spp. infections in this population, and (3) compare oral mycobiota with selected bacteriobiota strains during the observation in the ICU. We recruited 56 adult COVID-19 patients who qualified for mechanical ventilation. Patients received either standard or extended oral care procedures with tooth brushing. Oral samples were taken first within 36 h and after 7 days of intubation. Yeast-like fungi were identified by MALDI/TOF mass spectrometry. Yeast infection cases were retrospectively analyzed. spp. in oral sampling was identified in 80.4% and 75.7%, in 57.1% and 61.1%, and - species in 48.2% and 47.2% patients at baseline and follow-up, respectively. There were no differences in the overall CFU counts of spp. species and individual species in oral samples, both at baseline and follow-up. At baseline, a higher prevalence of spp. was associated with a higher identification rate of spp. (64.4% vs. 27.3%, = 0.041). At follow-up, there was a borderline lower prevalence of spp. in patients with spp. identified (57.1% vs. 87.0%, = 0.057). The incidence rate of candidiasis was 5.4% and the incidence density was 3.1/1000 pds. In conclusion, species in oral samples were identified in nearly half of patients. Oral health was moderately impaired. A high incidence of yeast infections, including invasive cases, in patients hospitalized in the ICU due to COVID-19 and requiring mechanical ventilation was noted. Severe COVID-19 and disease-specific interventions within the ICU possibly played a major role promoting spp. infections.