Abstract: In order to understand the relationship between strains from different origin, the genetic differences were explored between different strains.This study focus on using molecular techniques to analyze the DNA genetic phylogenetic of tomato canker pathogenic bacteria which collected from different areas, comparing the similarity of 43 strains by Blast method. The results showed that the 43 strains from different origin all were tomato canker pathogenic bacteria and the similarity was more than 99%. And the strains collected from the same area and year, especially the same tomato variety were almost clustered on the one branch.