We assessed the phylogenetic structure of tropical peat swamp forest to clarify the community assemblages in tropical peat swamp forest vegetation. We laid out six plots along the gradient of peat depth in the upper catchment of the Sabangau river, Central Kalimantan, Indonesia and investigated forest phylogenetic structure. As a comparison, we also investigated the phylogenetic structure of Sumatran peat swamp forest communities. We found a tendency for phylogenetic diversity to decrease as peat depth increased in both locations. Overdispersion in forest zones closest to rivers could be attributed to competitive exclusion in a relatively benign peatland environment, whilst underdispersed communities far from rivers could be attributed to the filtering effect of a more stressful environment. There was, however, unexpected underdispersion in the tall interior community in the Sabangau forest, where environmental conditions were less extreme. This observed underdispersion is possibly related to the history of peat development in this location as the ombrogenous peat is undergoing long-term oxidation due to reduced precipitation and lowering of the water table. We conclude that not only environmental filtering but also biotic filtering through such mechanisms as competitive exclusion contribute to the catenary sequence of tropical peat swamp vegetation.