The Pectobacterium atrosepticum strain SCRI1043 genome contains two complete prophage sequences. One, ECA41, is Mu-like and is able to integrate into, and excise from, various genomic locations. The other, ECA29, is a P2 family prophage, and is also able to excise from the genome. Excision of both prophages is rare and we were unable to induce lysis of cultures. Deletion of the entire prophages, both separately and in combination, did not affect the growth rate or the secretion of plant cell wall-degrading enzymes, but swimming motility was decreased. The virulence of prophage deletion strains in the potato host was decreased.