Shellfish cultured in Chile were analyzed to detect the presence of diseases notifiable to OIE (Office International des Epizooties: the World Organization for Animal Health). Tissue samples of the susceptible species, the abalones Haliotis discus hannai, H. rufescens, and oysters Crassostrea gigas, and Ostrea chilensis cultured in Chile were collected in winter and summer. Histological sections were performed of all species; furthermore, tissue from the Chilean oyster (O. chilensis) was processed for transmission electron microscopy (TEM) to describe the Bonamia-like protozoan detected in the haemocytes of some oysters. The only pathogen from the list of notifiable diseases of the OIE was Xenohaliotis californiensis in H. rufescens. This bacterium formed intracellular inclusions in digestive epithelia, mainly in the post-esophagus and digestive gland. The ultrastructural description of the Bonamia -like protozoan shows it is similar in some features and different in others from the species B. ostreae. and B. exitiosa included in the list of notifiable diseases of the OIE.