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Over 90% of juvenile salmon migrating from freshwater into the ocean will die before returning to freshwater to spawn, and disease may be a significant factor contributing to this mortality, however not enough is known about what the disease agents are. This multi-phase project was initiated to investigate this high mortality rate noted in the 2012 Cohen Commission Report on the decline of Fraser River Sockeye Salmon. In Phase 1, the project obtained collections of wild, hatchery and aquaculture salmonids from southern BC and provided a tissue inventory for assessment of microbes carried both by wild and cultured salmon in BC. During Phase 2a, the team developed, evaluated, and demonstrated the application of a sensitive, broad scale and high throughput genomic platform for the identification and quantification of important viral, bacterial, protozoan and fungal pathogens that may influence the health and survival of native populations of BC salmon. In addition, the project described the distribution of these microbes in wild and cultured salmon populations, potentially sharing transmission pressures and exchange of these microbes in Pacific aquatic ecosystems. The project is currently in Phase 2b which involves design and implementation of a surveillance study that will describe the presence, prevalence and loads of microbes in Southern BC Chinook, Coho and sockeye salmon smolts. This program will provide the most comprehensive study yet of the temporal and spatial distribution patterns and diversity of microbes in BC salmon, and their potential to negatively impact productivity of wild and cultured populations.