The microbiome community consists of microbes living in or on an organism and has been implicated in both host health and function. Environmental and host-related drivers of the microbiome have been studied in many fish species, but the role of the host genetic architecture across populations and among-families within a population is not well characterized. Here, Chinook salmon (Oncorhynchus tshawytscha) were used to determine inter-population differences and additive genetic variation within populations for gut microbiome diversity and composition. Specifically, hybrid stocks of Chinook salmon were created by crossing males from eight populations with eggs from an inbred line of self-fertilized hermaphrodite salmon. Based on high-throughput sequencing of the 16S rRNA gene, significant gut microbiome community diversity and composition differences were found among the hybrid stocks. These differences likely reflect divergent selection shaping the gut microbiome and its co-evolution with the host. Furthermore, additive genetic variance components varied among hybrid stocks, indicative of population-specific heritability patterns, suggesting the potential to select for specific gut microbiome composition for aquaculture purposes. Determining the role of host genetics in shaping their gut microbiome has important implications for predicting population responses to environmental changes and will thus impact conservation efforts for declining populations of Chinook salmon.