I can't remember which episode it was but Sisko threatened genocide against the Maquis and then immediately carried out the threat. In short he launched some bio weapon which would kill all inhabitants of a planet and leave it incapable of supporting life for 50 years. You can find the clip here: It is unclear how many casualties there were from Sisko's actions. I was disappointed that they did not follow up on this in latter episodes. Do note that I am only up to S06E16.