The aim of this study was to observe the microbiome on the skin-mucus of farmed Atlantic salmon (Salmo salar), before and after physical stress. The microbial community in the rearing water was additionally monitored, to explore potential interaction to the mucus microbiome. This study highlights the importance of clarification on the mucus microbiome interactions associated to stress events, as stress is considered as one of the main challenges in aquaculture.