Fungi have a primary role in the decomposition of organic matter in tropical peatlands and contribute to maintaining ecosystem functions. Understanding the belowground fungal diversity and composition is a preliminary step to predicting the stability of ecosystem functions, especially in ecosystems that have been exposed to anthropogenic impacts. This study determined soil fungal diversity and community composition in two types of forest: Peat swamp forest (PSF) and logged-over secondary forest (LOF) and a managed ecosystem (oil palm plantation, OPP) in peatland in Sarawak, Malaysia. Fungi from peat samples were isolated and identified using 18S rDNA region sequencing. Fungal diversity was calculated, and Bray-Curtis dissimilarity was performed to compare fungal communities between the study sites. LOF has the highest diversity, followed by PSF and OPP. In addition, the fungal community composition is more similar between LOF and PSF than between the peat forests and OPP. Aspergillus spp. and Trichoderma spp. contributed to the great dissimilarities between the peat forests and the managed ecosystem due to their dominance. In conclusion, LOF is an important ecosystem that retains relatively high fungal diversity. Different fungal communities were observed, which contained ecologically important fungal groups incorporated into the peat forests and an oil palm plantation.