Samples of rhizosphere soil and bulk soil were collected from under Araucaria bidwillii in a tropical montane rainforest at Mount Lewis forest reserve, Queensland, Australia. DNA was extracted from soil and denaturing gradient gel electrophoresis (DGGE) profiles of PCR-amplified partial rDNA internal transcribed spacer (ITS) regions of rhizosphere and bulk soil samples compared. Neither canonical analysis of the principal coordinates nor principal component analysis revealed clear separation of soil samples according to their origin in rhizosphere or bulk soil. Following amplification of rDNA ITS regions using the primers ITS1-F and ITS4, restriction fragment length polymorphism (RFLP) and sequence analyses were also used to identify fungal sequences that were present in clone assemblages from rhizosphere soil and bulk soil. A total of fifty-three RFLP types were thus identified, with the majority being ascomycetes and the remainder basidiomycetes or zygomycetes. Nine RFLP types had affinity with Mortier-ellaceae, and phylogenetic analysis indicated that these probably represent multiple Mortierella species in both rhizosphere and bulk soil samples. Similar evidence was obtained for the presence of multiple Trichosporon species. RFLP type 53 from a bulk soil sample was identified as a Soil Clone Group I ascomycete, confirming the widespread occurrence of this group.