Abstract. Two outbreaks of mortality in juvenile barramundi (Lates calcarifer) with a high prevalence of gastrointestinal cryptosporidiosis are described. Juvenile barramundi at a separate hatchery and grow-out facility were demonstrating markedly increased mortality rates. Histological examination in all cases indicated a heavy infection of Cryptosporidium-like organisms within the distal stomach and proximal small intestine. Electron microscopy confirmed a diagnosis of cryptosporidiosis; however, speciation was not possible.