Bursaphelenchus xylophilus has been recognized as a causal pathogen of pine wilt disease (PWD). In order to identify relevant molecular biomarkers, we selected a variable region of endo-${eta}$-1,4-glucanase (${eta}14-gcn$) which was cloned from the cDNA of B. xylophilus and B. mucronatus. We then identified three novel ${eta}14-gcn$ isoforms: $Bm-{eta}14-gcn;and;Bm-{eta}14-gcni$ from B. mucronatus, and $Bx-{eta}14-gcn$ from B. xylophilus. $Bm-{eta}14-gcn;and;Bx-{eta}14-gcn$ were found to be identical, whereas $Bm-{eta}14-gcni$ was unique to B. mucronatus. These isoforms are Bursaphelenchus-specific and may be employed as molecular markers for the diagnosis of PWD. Our phylogenetic analysis showed that these ${eta}14-gcns$ from Bursaphelenchus species were associated most closely with fungal ${eta}14-gcns$.