Branchiomyces in carp gills is usually localized in the blood vessels, the efferent branchial vessels and the capillaries, producing branched coenocytic hyphae capable of producing aplanospores by endogenous cleavage. In eels branchiomycosis hyphae and spores spread to visceral organs. Infection is probably by spores liberated from the necrotic tissue, but the exact route by which fish contract infection is unknown.
Infection in the blood vessels of the gill causes blockage, haemostasis and thromboses which consequently cause extensive necrosis of the gill filaments. Areas of the gill filaments turn brown, due to haemorrhages and thromboses, and grey as a result of ischemia. The process is fast and is accompanied by proliferation of the gill epithelium with resulting adhesions of the filaments. In eels, lesions containing hyphae and spores occur in the epicardium and the spleen.
Branchiomycosis occurs in eutrophic ponds with a high load of organic matter, ponds fertilized by organic manure, and water temperatures above 20°C. During the hot season, when ambient water temperatures are above 25°C, infection may spread to most fish in the pond and cause heavy mortalities.