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To examine the role of soil properties in influencing tropical fungal communities, soils were collected from Barito Ulu in central Borneo across an edaphic gradient ranging from clay-rich ultisols to sandy spodosols and from the upper and lower horizons and were subjected to high-throughput Illumina sequencing of the ITS1 region. The fungal community was clearly distinct between contrasting soils and depths, but the diversity metrics did not show significant differences. Differentiation by depth was more marked as the soils became less fertile. There were few marked impacts on fungal phyla or functional guilds at a broad level, but Ascomycota were more abundant in less acidic soils with a narrower C:N ratio. The forests of South-east Asia remain an underexplored frontier for fungal diversity studies.