A survey of the endophytic fungi in fronds of Livistona chinensis was carried out in Hong Kong. The endophyte assemblages identified using morphological characters consisted of 16 named species and 19 ‘morphospecies’, the latter grouped based on cultural morphology and growth rates. Arrangement of taxa into morphospecies does not reflect species phylogeny, and therefore selected morphospecies were further identified based on ribosomal DNA (rDNA) sequence analysis. The 5.8S gene and flanking internal transcribed spacers (ITS1 and ITS2) regions of rDNA from 19 representative morphospecies were amplified by the polymerase chain reaction and sequenced. Phylogenetic analysis based on 5.8S gene sequences showed that these morphospecies were filamentous Ascomycota, belonging in the Loculoascomycetes and Pyrenomycetes. Further identification was conducted by means of sequence comparison and phylogenetic analysis of both the ITS and 5.8S regions. Results showed that MS704 belonged to the genus Diaporthe and its anamorph Phomopsis of the Valsaceae. MS594 was inferred to be Mycosphaerella and its anamorph Cladosporium of the Mycosphaerellaceae. MS339, MS366, MS370, MS395, MS1033, MS1083 and MS1092 were placed in the genus Xylaria of the Xylariaceae. MS194, MS375 and MS1028 were close to the Clypeosphaeriaceae. MS191 and MS316 were closely related to the Pleosporaceae within the Dothideales. The other 5 morphospecies, MS786, MS1043, MS1065, MS1076 and MS1095, probably belong in the Xylariales. The value of using DNA sequence analysis in the identification of endophytes is discussed.