Sterile mycelia isolated from Pinus tabulaeformis were grouped into white morphotype strains based on cultural characteristics. Eighteen of the isolates were randomly selected and identified to various taxonomic levels based on nuclear ribosomal DNA (nrDNA) sequence analysis. The 5.8S gene and flanking internal transcribed spacer (ITS1 and ITS2) regions of nrDNA were amplified and sequenced. Phylogenetic analysis of the 5.8S gene sequences indicated that the white morphotype strains were Ascomycota. Further identification was achieved by means of sequence similarity comparison and phylogenetic analysis of the ITS regions. Results showed that strains WMS9 and WMS10 were Lophodermium species (Rhytismataceae), while strains WMS11, WMS13 and WMS18 were species of Rhytismataceae. Strains WMS2, WMS3, WMS4, WMS5 and WMS6 were identified to Rosellinia, strain WMS1 to Entoleuca, and strain WMS14 to Nemania (Xylariaceae). Strains WMS7, WMS8, WMS12, WMS15, WMS16 and WMS17 were xylariaceous species. The potential of using DNA sequence analysis in the identification of endophytic fungi is discussed.