Aims This study focused on intestinal microbiome variation across the phylogeogrpahic divide of rainbow trout and its potential functional effects on ocean migration. Methods and Results Hindgut intestinal contents were analysed using the 16S V4 hypervariable ribosomal gene region. Core microbiome taxonomies and overall microbial diversity were identified across the species phylogeographic divide with increased diversity found in Eastern Cascade fish. To determine potential functional differences between groups PICRUSt metagenomics analysis was utilized, revealing significant enrichment of lipid and fatty acid metabolism genes in Western Cascade fish microbiomes. Conclusions Decreased levels of intestinal microbial lipid metabolism in Eastern Cascade rainbow trout suggests increased lipid absorption in these fish given the consistent diets. Such absorption, and potential storage, would be an evolutionary benefit for increased migration distances experienced by Eastern Cascade fish. Core microbiome differences, and their functional associations, suggest evolutionary differences at the genetic level noticeably contribute to intestinal microbial community diversity. Significance and Impact of the Study The possibility of genetic variation controlling intestinal microbiome diversity could have significant impacts on strain selection for rainbow trout aquaculture, especially given the consistent rearing conditions experienced in our sample populations likely result in differences in intramyocellular lipid storage.