We compared genetic variations in virulence mega plasmids pXO1 and pXO2 of twenty-seven Bacillus anthracis strains from Korean patients and environmental samples together with those of Bacillus anthracis Sterne, Pasteur and A2012 standard strains. Genetic variations were analyzed in twenty-three variable regions (ten and thirteen variable-number tandem repeats and insertion/deletions in pXOl and pXO2, respectively). The pXO1 plasmids were classified into 7 groups and pXO2 plasmids to 12 groups. Discrete phylogenic lineages could be differentiated between environmental and clinical strains by UPGMA (unweighted pair group method with average) method. In addition, clinical strains showed more variations than environmental isolates. The pXO2 plasmid appeared genetically more unstable than pXO1. A general plasmid genotype could be suggested for Korean soil isolates since they mostly clustered into a representative group.