The present study aims to describe, with 16S DNA metabarcoding, the distal gut microbiota of a captive-reared population of juvenile Atlantic salmon (approx. one-year-old) with individual fish affected at different degrees by an external parasitosis, and the effect of formalin treatment on the gut microbial composition. This study provides new insight into both disease and treatment-related alteration of a healthy salmon gut microbiome when reared in captivity.