The plant pathogen Pseudomonas syringae pv. phaseolicola, which causes halo blight disease of beans, contains a 106kb genomic island PPHGI-1.  PPHGI-1 carries a gene, avrPphB, which encodes an effector protein that triggers a resistance response in certain bean cultivars. Previous studies have shown that when PPHGI-1 is excised from the bacterial chromosome avrPphB is down regulated and therefore the pathogen avoids triggering the host’s defence mechanism.  Here we investigate whether the down regulation of avrPphB is caused by supercoiling of PPHGI-1.  We also investigate the effect of a PPHGI-1 encoded type 1A topoisomerase, TopB3, on island stability and the pathogenicity of the bacteria in the plant.  Supercoiling inhibitors significantly increased the expression of avrPphB but did not affect the excision of PPHGI-1.  An insertional mutant of topB3displayed an increase in avrPphB expression and an increase in PPHGI-1 excision as well as reduced population growth in resistant and susceptible cultivars of bean. Together these results suggest an important role for topoisomerases in the maintenance and stability of a bacterial encoded genomic island and demonstrate that supercoiling is involved in the down regulation of an effector gene once an island has been excised, allowing the host defence response to be avoided.