Epitheliocystis is a condition affecting the gills and skin of fish, which has been reported from more than 50 freshwater and marine species. It is caused by intracellular Gram-negative bacteria. Mortalities have been associated with epitheliocystis infections in cultured fish. This review provides an update of our current understanding of this condition, including characterization of the pathogen using immunohistochemical and molecular studies. In most fish species the epitheliocystis agent was negative to an antibody specific for chlamydial genus-specific lipopolysaccharide antigen. Recently, four epitheliocystis agents from four different fish species have been characterized using molecular analysis. While they all belong to the order Chlamydiales, in a lineage separate from the Chlamydiaceae, they are distinct organisms and similarity analysis showed that they had highest similarity values with other chlamydia-like bacteria isolated from various sources, including humans or pig. This confirms the high diversity and host specificity of the pathogen. Further molecular analysis should result in an increased understanding of this condition. To date the pathogen has not been cultured, making experimental studies difficult. High stocking densities, presence of nutrients, season, temperature and fish age have been identified as potential risk factors for the manifestation of this condition.