Fish gills are in intimate contact with the aqueous environment. In intensive aquaculture production, variable physical and chemical water parameters, high stocking density, and husbandry procedures can disrupt the homeostasis of commensal and pathogenic microbiota on the gills. This has the potential to impact fish welfare and increase susceptibility to gill damage. This study investigated the relationship between microbial community profiles and gill pathology during a production cycle of Atlantic salmon in two commercial hatcheries. Relationships between gill histology, environmental conditions, and microbiome were determined using high-throughput data, including 16S rDNA amplicon sequencing data, histopathology data, and water quality parameters. Hatchery A used riverine water and operated a mixed system of recirculation aquaculture system (RAS) and flowthrough. Hatchery B used bore water and operated a RAS. Melanin deposits, hyperplastic, and inflammatory lesions were observed in the gills using histology. A higher prevalence of melanin deposits was detected and correlated to a change in beta diversity of bacterial communities in early time points (fingerling and parr stages). High abundance of Sphaerotilus sp., Pseudomonas sp., Nitrospira sp., Exiguobacterium sp., Deinococcus sp., and Comamonas sp. was correlated with a high prevalence of melanin in filaments. Bacterial diversity increased as the fish cohort transitioned from RAS to flowthrough in hatchery A. This study describes the major associations between gill histology and commensal microbiome of Atlantic salmon under commercial conditions