The diversity of ectomycorrhizal mycobionts of Pisonia grandis (Nyctaginaceae) from coral cays in the Capricorn-Bunker group, Great Barrier Reef, Australia, was examined. Only two ectomycorrhiza morphotypes (brown and black) were identified in soil from seven cays and DNA from both morphotypes was subjected to ITS-RFLP and sequence analysis. The brown morphotype was present in soil from all cays but the black morphotype was only observed in soil from three cays. ITS-RFLP analysis showed that the brown and black morphotypes were formed by different fungal taxa, with the RFLP pattern for the black morphotype being consistent with that of the culture previously obtained from black ectomycorrhizal roots on Heron Island. Comparison with the GenBank database revealed that closest matches to both morphotypes were sequences for various Thelephoraceae (Basidiomycota), but the brown and black morphotypes had only 80% sequence similarity to each other. Neighbour-joining analysis of these sequences with sequences for other Thelephoraceae grouped the brown and black morphotypes in a well-supported clade with several Tomentella species, suggesting that both belong to this genus. The data are discussed in relation to ectomycorrhizal fungal diversity and the coral cay habitat.