| Summary: | Complex gill disorder (CGD) is an important condition in Atlantic salmon aquaculture, but the roles of the putative aetiological agents in the pathogenesis are uncertain. A longitudinal study was undertaken on two salmon farms in Scotland to determine the variations in loads of CGD-associated pathogens (<i>Desmozoon lepeophtherii</i>, <i>Candidatus</i> Branchiomonas cysticola, salmon gill pox virus (SGPV) and <i>Neoparamoeba perurans</i>) estimated by quantitative PCR. In freshwater, <i>Ca.</i> B. cysticola and SGPV were detected in both populations, but all four pathogens were detected on both farms during the marine stage. <i>Candidatus</i> B. cysticola and <i>D. lepeophtherii</i> were detected frequently, with SGPV detected sporadically. In the marine phase, increased <i>N. perurans</i> loads associated significantly (<i>p</i> < 0.05) with increases in semi-quantitative histological gill-score (HGS). Increased <i>Ca.</i> B. cysticola load associated significantly (<i>p</i> < 0.05) with increased HGS when only Farm B was analysed. Higher loads of <i>D. lepeophtherii</i> were associated significantly (<i>p</i> < 0.05) with increased HGS on Farm B despite the absence of <i>D. lepeophtherii</i>-type microvesicles. Variations in SGPV were not associated significantly (<i>p</i> > 0.05) with changes in HSG. This study also showed that water temperature (season) and certain management factors were associated with higher HGS. This increase in histological gill lesions will have a deleterious impact on fish health and welfare, and production performance.
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