The nematode Bursaphelenchus xylophilus is the causal pathogen of pine wilt disease in Korea. Currently, it is reported that B. mucronatus also has a low pathogenicity. Despite this difference in pathogenicity, it is very difficult to differentiate these two species due to similarity in morphological characters. The sequence variation of internal transcribed spacer (ITS) and intergenic spacer (IGS) regions of ribosomal DNA has been used for species identification and phylogeny of B. xylophilus and B. mucronatus. But, the IGS region sequence data of B. mucronatus has been only reported in Portugal. In this study, We analyzed genetic variation on ITS and IGS regions of B. xylophilus and B. mucronatus (Asian genotype, European genotype) based on rDNA gene sequences, and conducted phylogeography using TCS network. When the each isolates was determined the phylogenetic analysis using the neighbor-joining method, Bursaphelenchus species were divided into each groups, and showed low variation within each species. In the TCS analysis, The isolate of B. xylophilus and B. mucronatus (Asian genotype and European genotype) were divided into each groups and confirmed slightly genetic distance within species. B. mucronatus European genotype has possibility of new species different with Asian genotype.