Eukaryotes are ubiquitous and play critical roles in food web dynamics, global carbon and nutrient cycle. Possessing multiple nutritional modes, eukaryotes play key roles as producers, decomposers, parasites, and predators. Little is known about the composition and diversity of eukaryotes in the different tropical peat ecosystems and how land-use change affect them. In this study, next generation sequencing was used for sequencing within the 18S rDNA gene to analyse the differences in the diversity and relative abundance of eukaryotes types. The finding indicated, in the dry month of April 2012, the operational taxonomic unit for eukaryotic community for peatland at Maludam National Park was low (986), high for logged over peatland Cermat Ceria (1853) and 7 years old oil palm plantation (1677) at Durafarm, Sri Aman, Sarawak and decreased to 865 for 11 years old oil palm at Naman, Sibu, Sarawak, Malaysia. Similarly, the α-diversity of eukaryotic community indicated species per sample ID at Maludam was low (65), high (450) for loggedover peatland and Durafarm (400) and Naman (200). Total phyla was highest, 28 for oil palm plantation at Durafarm, 27 for logged-over peatland, 23 for Maludam and 20 for Naman. The taxonomic composition of eukaryotic community indicated the population at the peatlands comprised mainly of fungi and other unclassified eukaryotes. While under the matured oil palm plantations, the predominant eukaryotic kingdom was fungi. The common fungal phyla for all peat ecosystems were Ascomycota, Basidiomycota, Fungi incertae sedis and Chytridiomycota. Ustilaginomycota being dicot parasitic fungi, was found in the peatlands at Maludam and Cermat Ceria but absent in oil palm plantations. Blastocladiomycota was absent in Maludam National Park but present in all other peat ecosystems. While, Glomeromycota and Neocallimastigomycota were present in logged-over peatland. The fungal population increased in the oil palm cultivated areas because of the absence of water logged area, drainage system for water management, presence of abundant organic biomass, high rainfall, soil acidity and soil moisture content. On the contrary, the minor predatory, autothropic and parasitic Alveolata, Nuclearidae and Fonticula, Rhizaria, Stramenopiles and Amoebozoa decreased with drainage and cultivation of oil palm and reduction of aquatic flora and fauna. The impacts of human activities such as construction of drainage system, logging and cultivation of oil palm resulted in obvious increase in the eukaryotic biodiversity due to abundant organic biomass and reduction in water logged peat. As the oil palm reached the aged of 11 year the eukaryotic biodiversity declined, probably due to peat compaction and reduction of decaying organic matters.