Francisellosis, caused by the bacterium Francisella noatunensis, is one of the most severe diseases affecting farmed cod, and has caused great economic loss for the cod farming industry in Norway. We studied the fate of F. noatunensis in the marine environment, focusing on the role of blue mussels. In experimental challenges, waterborne F. noatunensis was rapidly filtered by the blue mussel and transported to the digestive diverticulae. The bacteria passed through the entire digestive system. Intraperitoneal injection of cod with suspensions prepared from faeces collected from challenged mussels resulted in the development of francisellosis in the recipients, demonstrating that some bacteria were alive and infective when shed in mussel faeces. Bacterial clearance from the mussels was relatively fast, and no evidence was found, suggesting that the bacterium is capable of persisting or multiplying in the mussel tissues. A cohabitation experiment with cod and mussels previously exposed to F. noatunensis did not lead to infection in cod. A direct transmission from contaminated mussels to cod was thus not demonstrated; however, faeces particles with infective bacteria may play a role in the transmission of the bacterium in marine food chains.