Magnusiomyces capitatus is an emerging opportunistic yeast in the Mediterranean region. We report from Nepal one case of M. capitatus infection and six other cases of colonization/probable infection due to M. capitatus at a tertiary care center. Majority of the patients were immunocompromised, at extreme age, associated with comorbidities, and had history of close contact with livestock and poultry. The isolates were identified by phenotypic and genotypic (ITS and D1/D2 region of 26S rDNA sequence) methods. Molecular typing of the isolates was carried out by amplified fragment length polymorphism. Minimum inhibitory concentration (MIC) of the isolates for amphotericin B, caspofungin, fluconazole, itraconazole, voriconazole, posaconazole, anidulafungin, and micafungin were 2, 0.1–4, 2, 0.12–0.5, 0.12–0.5, 0.25, 1–4, and 1–4 μg/ml, respectively. Presence of M. capitatus infection was not known in Nepal, and the study should alert the clinicians and infectious disease specialists.