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Cultured juvenile silver perch, Bidyanus bidyanus (Mitchell), were affected by epitheliocystis, with a prevalence of up to 75%. The condition affected 2–96% of gill filaments. Granular basophilic cysts ranged from 10 to 87 μm and had a round‐to‐oval shape. The infected cells were positioned centrally within a lamella, often close to its tip, and their identity was difficult to determine, but the involvement of pillar cells could not be precluded. The size of pathogen was within the range previously reported. The pathogen had two morphological forms, which were positioned differently within the cyst. The form located more in the centre was rod‐shaped with an electron‐dense core and electron‐lucent vesicles on the sides of the core. Its mean length was 498.14 nm (SD = 47.68 nm), and its mean width was 145.14 nm (SD = 9.53 nm). The form present in a more peripheral position had an irregular shape, often did not show the electron‐dense core and did not have the electron‐lucent vesicles. Its mean length was 704 nm (SD = 170.29 nm) and its mean width was 152.4 nm (SD = 16.40 nm). Both forms were enclosed by a double trilaminar membrane. This is the first confirmed report of epitheliocystis in Australian freshwater fish.