This work describes the characterization of the causal agent of disease outbreaks that, from 1999, occurred repeatedly during the summer months (temperatures higher than 15 degrees C) in Atlantic salmon (Salmo salar) cage-farmed in Chile affecting both smolts and adult fish cultured in estuary and marine waters, reaching in some occasions a cumulative mortality up to 25% of the affected population. Diseased fish showed exophthalmia with accumulation of purulent and haemorrhagic fluid around eyes, and ventral petechial haemorrhages. At necropsy, haemorrhage in the abdominal fat, pericarditis, and enlarged liver, spleen and kidney are common pathological changes. Gram-stained smears revealed the presence of Gram-positive cocci, beta-hemolytic, negative for oxidase and catalase tests. Although biochemical characterization of the isolates using the miniaturized system rapid ID 32 Strep suggested their assignation to genus Gemella, sequencing and RFLP analysis of the 16S rRNA revealed that bacteria associated with the mortalities belong to Streptococcus phocae. Serological studies demonstrated that all the salmon isolates are antigenically homogeneous, which can facilitate the development of preventive measures and, although sharing some antigenical determinants, they belong to a different Lancefield group than the type strain isolated from seals. On the basis of these facts, we conclude that the species S. phocae is an emerging pathogen for salmonid culture in Chile, and it should be included as a new member of the warm water streptococcosis. (c) 2007 Elsevier BN. All rights reserved.