The pinewood nematode (PWN, Bursaphelenchus xylophilus) is known to be a major pathogen of the pine wilt disease (PWD). However molecular pathology of B. xylophilus is not completely understood, the pathogenecity of PWD is related to cell wall-degrading enzymes such as endoglucanases, expansins and pectate lyases (PELs). Recently, we developed stage-specific expressed tag library of B. xylophilus and identified a novel PEL, Bx-PEL3. We cloned Bx-PEL3 gene with RT-PCR, which showed high similarity to previously reported Bx-PELs. Phylogenetic analysis revealed that PEL3 was much closer to PELs of B. xylophilus than any other PELs. PEL3 has a conserved intron site as found in Bx-PEL2 in the genomic DNA analysis. Quantitative real-time PCR analysis revealed that Bx-PEL1 and Bx-PEL2 were more predominantly expressed than the Bx-PEL3 in B. xylophilus. The difference of expression level among Bx-PELs according to growth condition suggests that each Bx-PEL plays different biochemical role in the pathogenesis of the PWD.