Atlantic salmon undergo dramatic physiological changes as they migrate from freshwater to the marine environment. Osmoregulatory adaptation is the most crucial change, necessitating functional adaptations of the gills, kidney and intestine. Additionally, novel pathogens, microbes and dietary items are encountered in the saltwater environment, which suggests major changes in the intestinal microbiota following movement to saltwater. Here we compared the intestinal microbiota harboured in the distal digesta of Atlantic salmon freshwater fish (FW) kept in a commercial Scottish freshwater hatchery with that of their full-siblings after seawater acclimatisation (SW) by a 16S rRNA (V3-V4) high-throughput sequencing approach. Alpha- and beta-diversity were found significantly higher in FW compared to SW, both in terms of richness and diversity. Metastats analysis identified a higher number of Operational Taxonomic Units (OTUs) unique to FW compared to SW, with an additional 238 OTUs found at significantly different abundance. A core microbiota of 19 OTUs was identified in 100% of all fish, which indicates that certain microbes are maintained to fulfil minimal functions within the gut. Furthermore we show that the uniqueness of the respective microbial profiles can be correlated with significant differences in KEGG pathways including lipid and amino acid metabolism.