1 ITS-RFLP and sequence analysis of endophytes from Acianthus, Caladenia and Pterostylis (Orchidaceae) in south eastern Queensland, Australia. Bougoure J.J. 1 , Bougoure D.S. 2 , Cairney J.W.G. 2 and Dearnaley, J.D.W. 3, 1 School of Plant Biology, Faculty of Natural and Agricultural Sciences, The University of Western Australia, Crawley 6009, Australia. 2 Mycorrhiza Research Group, Centre for Horticulture and Plant Sciences, The University of Western Sydney, Parramatta Campus, Locked Bag 1797, Penrith South DC, NSW 1797, Australia. 3 Department of Biological and Physical Sciences, The University of Southern Queensland, Toowoomba 4350, Australia. Author for correspondence: Fax +617 4631 1530; Email: dearns@usq.edu.au. In this study we have used ITS-RFLP and sequence analysis to determine the identities of the fungal endophytes of six terrestrial orchid species from south eastern Queensland, Australia - a region previously unexplored in this context. Pure cultures of orchid colonising fungi were obtained and fungal identities were assessed by means of ITS-PCR, RFLP analysis, sequence comparison and protocorm colonisation tests. ITS-PCR and RFLP analysis resulted in five main groupings. Sequencing and GenBank comparison of these five groups showed that the fungal endophytes isolated from the three Pterostylis species were probably Thanatephorus sp. There was close sequence identity (90%) of the fungus isolated from Acianthus spp. to Epulorhiza repens, suggesting these may be the same fungal species. However, the fact that only E. repens succeeded in colonising protocorms of Thelymitra pauciflora suggests these may be different species of Epulorhiza. Analysis of the ITS and LSU sequences of the fungus isolated from Caladenia carnea showed high identities with a sequence