This study was conducted to investigate diversity of fungi in potting media, organic fertilizers and compost using culture-based and pyrosequencing techniques. Fungal diversity was evaluated using serial dilution, direct plating and baiting with carrot slices, potato slices, radish seeds, cucumber seeds and cucumber cotyledons. Identity of the isolates was confirmed using sequences of the ITS rDNA. Direct plating technique was found superior over other culture-based techniques in the number of fungi detected. It was also found to be a simple and less time consuming technique. Comparing the efficiency of direct plating with pyrosequencing revealed that pyrosequencing detected 12 to 18 times more fungi from potting media (PM), organic fertilizers (OF) and organic composts (OC). Analysis revealed that there were rev vere differences between PM, OF and OC in the dominant phyla, classes, orders, families, genera and species detected. Evaluation of products from the USA and European and Asian countries revealed that they have different levels of contamination with pathogenic and saprophytic fungi. Trichoderma, Aspergillus and Penicillium were the most dominant fungi in all samples. Simplicillium spp., Cladosporium spp., Bionectria spp., Alternaria spp. and Fusarium spp. were recovered at different frequencies from samples of potting media. Fusarium spp. were recovered at high frequencies from samples of organic fertilizers, and organic and non-organic LU composts. Detection of plant pathogenic fungi in imported agricultural material raises concerns from risks associated with these materials. The evaluated methods in this study, especially direct plating and pyrosequencing, may be used as tools by quarantine officers to help detect and reduce entry of unwanted fungi into Oman.