We identified both the fungi and plants of ectomycorrhizal root tips of Dipterocarpaceae using the sequence of mitochondrial large (ML) subunit ribosomal DNA, internal transcribed spacer (ITS) sequence of nuclear ribosomal DNA, partial matK sequence of chloroplast DNA and trnL-trnF spacer sequence of chloroplast DNA. We compared the DNA sequences from ectomycorrhizal roots with the sequences from the available databases using phylogenetic analysis. The ectomycorrhizal fungi identified by ML and/or ITS sequences belonged to the following seven families: Russulaceae, Boletaceae, Cortinariaceae, Thelephoraceae, Hygrophoraceae, Sclerodermataceae, Cantharellaceae and Amanitaceae. The Dipterocarpaceae species identified by partial matK and/or trnL-trnF sequences belonged to the following genera: Dryobalanops, Hopea, Vatica, Cotylelobium, Anisoptera, Upuna, Dipterocarpus and Shorea. Members of Thelephoraceae, which have never been reported to form symbiotic roots with Dipterocarpaceae, appeared to be the most abundant and were usually associated with Shorea species. Analyses of other Dipterocarpaceae species are needed to confirm these results.