【Objective】 Jiangsu, Zhejiang, Anhui and Shandong, these four provinces in east China, are recognized as the initial occurrence of pine wilt disease in China. And east China is also the most suitable growth area for Bursaphelenchus xylophilus. Studying the genetic differentiation of the B. xylophilus population in those regions will provide important basic genetic information to establish a B. xylophilus epidemic source tracing system in China. 【Method】 Samples of B. xylophilus were collected from pine trees affected by pine wilt disease in east China, and strains were isolated and purified. The genomic deoxyribonucleic acid (DNA) of strains was extracted and sequenced. The number and types of single nucleotide polymorphism (SNP) loci and genotypes in each region were analyzed using bioinformatics software. Cluster analysis was used to compare the genetic differentiation among different strains based on SNP markers, while Treemix was used to detect gene penetration routes. 【Result】 A total of 67 B. xylophilus strains were isolated and collected in 60 county-level administrative regions of Anhui (AH), Fujian (FJ), Jiangsu (JS), Jiangxi (JX), Shandong (SD) and Zhejiang Province (ZJ) in East China. All strains were sequenced through the whole genome; genome calling analysis indicated 12 genotypes, of the 67 strains, where six types (i.e., A→G, C→G, C→T, G→A, G→C and T→C) occurred at a higher frequency than others. A total of 6 531 684 SNP loci were obtained and the number of SNP was different between strains. The number of SNP counts, homozygotes, missing SNPs, and private SNPs showed no significant regional differences among the six provinces, and there was no significant correlation with invasion time. Principal component analysis showed that 67 strains of B. xylophilus may be divided into three groups; each group had a specific correlation with a geographic origin. Most strains belonged to group 1, which included all strains from Zhejiang and Jiangxi, as well as most of strains from the other four provinces. Group 2 included 14 strains from Jiangsu, Anhui, Shandong and Fujian, and group 3 included only seven strains from Anhui, Fujian and Shandong provinces. Two gene migration routes detected by Treemix: ① group 2 of Jiangsu to group 1 of Anhui; and ② group 3 of Shandong to group 2 of Anhui. 【Conclusion】 There were abundant SNP loci in B. xylophilus in east China, where the SNP characteristics of different strains were relatively disparate, and there was no clear regularity between SNP diversity and invasion time. Overall, the B. xylophilus strains in east China may be divided into three groups, and there was a specific correlation between different groups and geographic areas. In the area where the 1-AH and 2-AH groups were located, there may have been re-invasion by strains from groups in other areas.