Factors affecting the establishment of an adult-like gut microbiota in marine environments remain largely unknown. In terrestrial animals, however, it is well established that the juvenile environment has a major impact on the gut microbiota later in life. Atlantic Salmon is an anadromous fish important in aquaculture with a juvenile freshwater stage, and an adult seawater stage. For wild salmon, there are major dietary changes with respect to availability of long-chain polyunsaturated fatty acids (LC-PUFA), with LC-PUFA being limited in freshwater. The aim of our work was therefore to determine the effect of a juvenile diet high LC-PUFA, as compared to diet low in LC-PUFA on the transition to an adult like gut microbiota for Atlantic Salmon.