Soil microbes are the unseen living organisms which are involved in various roles for oil palm productivity. Matured oil palm plantation peat soil may be inhabited by different bacterial populations compared to logged-over and primary forest. Thus, conversion of peat forests into oil palm plantations might cause changes in the prokaryotic population in soil. The differences in the prokaryotic population were analysed to assess the profile of the prokaryotic population in each ecosystem. In this study, Denaturing Gradient Gel Electrophoresis of the purified 16 rDNA amplicon (16S PCR-DGGE) was analysed. Berger-Parker and Shannon-Weaver Species Index indicated that Durafarm Plantation, DF (0.10, 8.05) had the most diverse soil population followed by Maludam primary forest, MD (0.11, 7.75) and Cermat Ceria loggedover forest, CC (0.19, 7.63). The 16S rDNA sequence analysis showed that all ecosystems were dominated by unclassified Bacteria (62%, 65%, 69%), followed by Acidobacteria (8%, 19%, 4%), Actinobacteria (8%, 6%, 12%), α-Proteobacteria (8%, 3%, 8%) and Firmicutes (5%, 2%, 2%), respectively for MD, CC and DF. Increased number of species was recorded in Durafarm Plantation with the emergence of the forest microbes such as Acidipila rosea, Acidimicrobium sp., Actinomycete sp., Mycobacterium sp., Afipia sp., Acetobacteraceae bacterium, Rhizobium sp., Rhodoplanes sp. and Sphingomonadaceae bacterium. It is interesting to note that planting oil palm on deep peat can assist in rejuvenating some bacterial population that were missing during forest clearing and thus contributing to the improvement of soil bacterial biodiversity.