Fungi are commercially important and play a critical role in global environmental health. There is considerable interest in applied fungal research, which includes commercial production of important compounds, human health, food safety and security and crop protection . Most research to date has focused on fungi that affect human health or have commercial applications. Comparatively little is known about many of the fungal species found in the environment. Analysing fungal community roles and identities in a novel environment is challenging due to the paucity of literature and lack of available sequences. The quality of fungal sequence databases is highly variable  and often lacks proper annotation and lineage designations ,. Amplifying the entire ITS region (including the 5.8S region) may be more phylogenetically informative, but may also artificially reduce microbial richness and bias community structure . In addition, the incidence of chimeric sequences also increases due to the conservation of the 5.8S region . In this study, both ITS1 and ITS2 were used for community analysis. Although, both sets of primers used for their amplification are biased for certain groups ,. In this study, the ITS2 region was found to be more sensitive in detecting novel OTUs, which could be due to the sample type or the biases and limitations of the primer sets ,,.