Atlantic salmon (Salmo salar L.) is threatened by Saprolegniosis, a disease caused by the water mould (oomycete) Saprolegnia. Introduction of beneficial microbes is proposed as a sustainable measure to control Saprolegniosis. Analyses of the microbial community of Atlantic salmon eggs revealed that these eggs house a variety of oomycetes, fungi and bacteria. Two bacteria that were isolated, a Frondihabitans species and a Pseudomonas species, inhibited growth of Saprolegnia and infection of salmon eggs, and growth-inhibiting chemical compounds produced by these bacteria were identified. Among the fungal community, both a quantitative and qualitative difference in the Trichoderma population between Saprolegnia infected and healthy salmon eggs was observed, which suggested that mycoparasitic Trichoderma species could also play a role in Saprolegnia suppression in aquaculture. In conclusion, Frondihabitans, Pseudomonas and Trichoderma species and/or their active chemicals, may be exploited to control Saprolegniosis and probably also other diseases in aquaculture and natural environments.