Whilst our understanding of patterns of fungal diversity is increasing, we have a paucity of data from tropical regions, and especially South-east Asia, to contribute to this. The island of Borneo is valuable in this regard as it contains high pedodiversity known to influence ecological communities. In this study, we examined soil fungal diversity and community composition using Illumina sequencing. We collected soils from Barito Ulu, in central Borneo, across an edaphic gradient from clay-rich Ultisols to sandy Spodosols and from upper and lower horizons. The fungal community was clearly distinct between contrasting soils, but diversity did not show such clear patterns. The fungal community also differed by soil depth and there was indications of lower diversity in deeper soil layers. Soil properties, in particular soil pH were a clear driver of differences in the fungal community. These patterns also differed depending on fungal lifestyle (e.g. saprotophs, ectomycorrhizal fungi). We present here one of the most detailed studies of soil fungi in tropical forests of Borneo.