The public health risk associated with the autopsy unit is high and information on indoor microbial air contamination is limited. Airborne pathogenic fungi thrive in moist indoor environments similar to autopsy room conditions. They spread through spores, cause infections in immunocompromised patients, and exhibit resistance to antimicrobials, making them a public health threat. This study profiled fungi circulating in the indoor air of a referral autopsy unit in Accra, Ghana. The different sections of the unit were sampled using the standard open plate technique. Fungal isolates obtained were phenotypically and molecularly characterized. The resistance to fluconazole and itraconazole, as well as a germicide used in routine cleaning of the unit, was tested using broth microdilution assays. Fungi isolated include species of clinically relevant strains of Candida and Aspergillus; also, Penicillium spp. and Mucor spp. They exhibited high levels of resistance to fluconazole and itraconazole, as well as Denzal® germicide used in routine cleaning of the autopsy unit. This study is the first to profile the fungal diversity of an autopsy unit in Ghana, and the findings suggest that workers might be exposed to fungi with high pathogenic potential that could cause infections.