Gill diseases are a growing health challenge in salmon farming worldwide, but many gaps remain in our knowledge. Gill diseases are generally complex and multifactorial disorders, often with presumable spatial and temporal distribution patterns, but are highly difficult to effectively prevent and control. The term complex gill disease (CGD) includes a wide range of clinical disease presentations on the gills of farmed salmon; usually, CGD presents from the end of summer to early winter. The pathogens involved include Neoparamoeba perurans, Tenacibaculum maritimum, Candidatus Piscichlamydia salmonis, Candidatus Branchiomonas cysticola, Desmozoon lepeophtherii (syn. Paranucleospora theridion) and viruses, such as the Atlantic salmon paramyxovirus (ASPV) and salmon gill poxvirus (SGPV). Amoebic gill disease (AGD) is perhaps the most significant disease in terms of gill health and economic impact. AGD results in high mortality, reduced production performance and impaired fish welfare. This review summarizes and analyses CGD research, outbreaks and treatment, with a focus on AGD, as well as on knowledge gaps and avenues for future research.