A study was conducted to investigate fungal diversity in organic compost originating from Oman. Analysis of diversity was conducted using 454 pyrosequencing and direct planting. The obtained fungal species through direct plating were identified based on the internal transcribed spacer region of the ribosomal RNA (rRNA). Pyrosequencing detected the presence of 94 fungal species, compared to 5 species detected by direct plating. Pyrosequencing also detected more fungal phyla, classes, orders, families and genera. Most of the detected species belonged to Ascomycota and Chytridiomycota, with Powellomyces spp., Eupenicillium spp. and Chaetomium spp. being the most dominant genera. The majority of the detected species (>99%) were found to be either saprophytic or with biocontrol characteristics, with few species (Fusarium and Phoma), being potential pathogens of plants. The low level of presence of pathogenic species may provide evidence of the health status of the organic compost. The study reports for the first time the occurrence of 67 fungal species in Oman. It discusses the superiority of pyrosequencing over direct plating and the factors influencing diversity of fungi in organic composts.