The war started a few decades ago by the Eurondans who wanted to eradicate the Breeders because they cultivated without any concern for genetic purity. The Eurondans released their first bombs on the Breeder nation to try to eradicate them.
Long before the war started, the Eurondans built an underground base. The war started after a man thought the Breeders spread like a plague on Euronda. (SG1: "The Other Side")