The critical role of the gut microbiome in supporting immune function, metabolic processes and somatic growth is well characterized in humans and terrestrial livestock species, however the role of the gut microbiome remains poorly elucidated in aquatic species. To this end we assembled the Rainbow Trout Microbial Genome Atlas (RTMGA) recovered from a highly domesticated farmed cohort (n = 118) originating from the USDA NCCCWA breeding program. A hybrid assembly approach combining 3.793 (Gb) of short, and long reads was employed, in tandem with in-vitro anaerobic culturing. A sum of 94 high quality bacterial genomes exhibiting a minimum completeness & contamination threshold of 70% and 10% respectively were taxonomically classified. We report 9 putative novel species identified, and 21 species, 8 genus and 53 family level taxonomic classifications, of which 7 genomes exhibited >99% completeness. Metagenomic functional profiling showed enrichment for short chain fatty acid production, acetate conversion to methane, and nitrogen metabolism in the anerobic gut macroenvironment. Comprehensive classification and functional interrogation of the Rainbow trout microbiome may assist in better capturing the breadth of commensal biochemical pathways underpinning commercially relevant phenotypes of interest.