Tropical peat swamp forests (TPSF) support enormous biodiversity and huge emergent trees despite their waterlogged, acidic and nutrient-depleted conditions. TPSF are presently subject to destruction and severe degradation due to drainage, logging, fire and agricultural conversion, however, the microbial ecology of these endangered ecosystem remains largely unknown. This study investigated the microbial diversity and composition in North Selangor peat swamp forest (NSPSF), Malaysia. Peat samples were obtained from three depths (surface, 45 cm and 90 cm) from around three common tree species in NSPSF – two emergent trees: Shorea uliginosa and Koompassia malaccensis (a nitrogen-fixing legume), and a palm Eleiodoxa conferta. Microbial diversity and composition were assessed through next-generation sequencing of 16S rRNA gene performed on Illumina MiSeq. Environmental parameters including water pH, dissolved oxygen, total nitrogen, total phosphorus, total phenolic contents and C/N ratio were found to be significantly different between depths, but not between tree species. The surface possessed the highest microbial diversity. Microbial diversity and composition were mainly influenced by the depth, but not the tree species, although tree species exhibited a small influence on the microbial composition at the surface and at 90 cm. Total nitrogen was found to be the core environmental parameter shaping the microbial composition in NSPSF. Proteobacteria was the dominant phylum, followed by Acidobacteria. The archaea displayed higher abundance with increasing depth, with Euryarchaeota as the most dominant phylum. Methanogenic archaea (class Thermoplasmata) were found more abundantly in deeper layers while methanotrophs (family Methylocystaceae) were more abundant at the surface. Rhodoplanes was the most abundant genus, and it is likely to be involved in nitrogen fixation. Ammonia-oxidizing archaea (AOA) were detected in the absence of ammonia-oxidizing bacteria (AOB), indicating that nitrification in TPSF is likely performed by AOA. The correlation analyses between the relative abundance of various phyla/classes/orders and environmental parameters revealed stronger impact of environmental parameters on the less-abundant microbial groups compared to the dominant lineages.