Spread of pathogens between species depends on the nature of the pathogen and risk factors for dissemination. Pathogenic agents can be introduced into aquaculture with biological material (for example fish and bivalves), water, equipment/feed that is transported into the fish farm, persons and scavengers and animals (for example cats and birds). Movement of hosts, vectors, latent carriers and contaminated water are all risk factors for the spread of pathogens. During filtration, bivalve molluscs may accumulate microbes that may be pathogenic for other species. Bivalve molluscs are known as vectors of both bacteria and viruses causing disease in humans. Also fish pathogenic bacteria and viruses have been found in bivalves, and it has been pointed out that bivalves must be considered potential reservoirs or vectors of fish pathogenic agents. The amount of information on fish pathogens in bivalves and potential fish-bivalve-fish transmission is rather limited. In general, pathogens do not cross phylum barriers. So far, all available information indicates that the bivalves are mechanical vectors of fish pathogens, as no replication or propagation has been documented. In severe cases, opportunistic bacteria might be pathogenic for both fish and bivalves, given the right doses and conditions. Although very few cross-infection trials have been carried out, it seems likely that fish pathogens in general are not pathogenic to bivalves and vice versa. There is however a need for relevant surveillance considering the risk of spreading fish diseases when moving bivalves. Control mechanisms that can be used to prevent the outbreak of disease in aquaculture include vaccination, fallowing, movement restrictions, good husbandry practices, site selection, chemotherapy and clearance of a farm.