【Objective】This study is focused on the genetic variations and population structures among different Bursaphelenchus xylophilus strains isolated from Guangdong Province using single nucleotide polymorphisms (SNPs) as markers. This work provided fundamental information for the establishment of a B. xylophilus tracking system in China.【Method】Thirty strains ofB. xylophilus from different regions of the Guangdong Province were collected and sequenced. Genome-wide SNPs were analyzed using bioinformatics, and population splitting events were discovered based on previous SNP data.【Result】Statistical analysis of SNPs across 30 B. xylophilus strains showed that the number of SNPs and homozygotes in seven of the 30 strains (GD01, GD09, GD12, GD20, GD22, GD24 and GD25) were less than the remaining 23 strains. The genotypes that occurred with a higher frequency in these seven strains were A->G, C->G, G->C, T->C, while the other 23 strains contained genotypes that were A->G, C->T, G->A, T->C. The strains from Guangdong Province could be divided into 3 populations based on PCA and hierarchical clustering.【Conclusion】The genetic diversity ofB. xylophilus population in Guangdong Province is relatively high; thus, it should have different sources through which genetic variation is introduced.