Abstract: Pine wilt disease caused by Bursaphelenchus xylophilus（Steiner & Buhrer）Nickle is a devastating major biological disaster. Since introduced into China in 1982, it has caused severe damage to pine forest resources, natural landscapes, and ecological environment, resulting in significant economic and ecological losses. In this study, SNP markers were used to investigate the genetic characteristics of B. xylophilus in Shandong Province. B. xylophilus populations from Liaoning Province （the northernmost region）, Guangdong Province （a widely studied region）, and Japan （a foreign region） were used as references. A total of 41 collected B. xylophilus samples were subjected to whole-genome resequencing. The degree of genomic variation among different populations was observed, the genetic characteristics of B. xylophilus in Shandong Province were explored from a molecular perspective, and the genetic relationships among B. xylophilus populations in Shandong, Guangdong, and Liaoning Provinces were investigated. The results showed that the B. xylophilus within Shandong Province belongs to the same population, which has a close genetic relationship with the population in Liaoning Province but exhibits significant differences from the population in Guangdong Province. Within Shandong Province, severe cross-infection occurs in coastal areas, with no obvious regional clustering characteristics. Additionally, the B. xylophilus populations in Shandong and Liaoning provinces are those with a significant founder effect. The results provide a theoretical basis for the transmission path, ecological adaptation, and disease prevention and control of pine wilt disease.