Abstract The pinewood nematode (PWN) Bursaphelenchus xylophilus is the causative agent of pine wilt disease and the greatest biological threat to conifer forests worldwide. Here we describe the near-complete mitochondrial DNA (mtDNA) sequence (12,945 bp) of the PWN lineage recently introduced in Europe. The absence of polymorphisms across the mtDNA of three Portuguese isolates suggests that a single mitochondrial lineage was introduced in southwestern Europe. We also found that Portuguese isolates have an incomplete stop codon (TA) at COX3, while the reference mtDNA from a South Korean isolate has a complete stop codon (TAA). Moreover, two insertion/deletion polymorphisms change the ND4 protein in a stretch of seven amino acids, and a polymorphic mononucleotide repeat alters the predicted structure of the tyrosine tRNA in different geographical isolates. Overall, the new PWN mtDNA sequence provides a basis for studying the European dispersion of this important invasive species.