The study aimed to compare the yeast species diversity in the specific environment of dishwashers, taking into account the potential risk for users. Yeasts were isolated from ten dishwashers and from tap water supplied to the appliances. Samples were collected for mycological analyses at the beginning of each month, from February to May 2016. Four dishwasher sites (rubber seals, detergent dispensers, sprinklers, and water drains) were analyzed. The microfungi were identified by the standard procedures applied in mycological diagnostics. To confirm species identification, molecular analysis was performed based on the sequences of the D1/D2 region. The presence of microfungi was detected in 70% of the investigated appliances. Rubber seals, detergent dispensers, and water drains were the most frequently colonized elements. Thirty-five yeast strains were isolated in this study, of which twenty-seven were obtained from dishwashers and eight from tap water. The strains belonged to six genera and six species (Candida parapsilosis, Clavispora lusitaniae, Dipodascus capitatus, Exophiala dermatitidis, Meyerozyma guilliermondii, and Rhodotorula mucilaginosa). Most of the strains came from rubber seals. In this way, it was demonstrated that the dishwashers’ condition is sufficient as an ecological niche for microfungi.