This paper gives an account of the pathogens found in the cultivated Japanese oyster Crassostrea gigas and in the mangrove oyster Crassostrea rhizophorae from natural populations of two sites, Sambaqui (27° 29′18″S, 48° 32′1″W) and Ribeirao da Ilha (27° 42′51″S, 48° 34′6″W), Santa Catarina Island, Brazil. Oysters were collected in March 2008 and April 2009, 150 per site, year and condition (rocky shore and culture). For pathological study, the techniques used were: macroscopic examination, histology and tissue culture in fluid thioglycollate medium specific for Perkinsus . The results showed the presence of the polychaete Polydora sp. with high prevalence (up to 100%) in C. gigas ; gametic hypertrophy in C. rhizophorae from Ribeirao da Ilha and in C . gigas from Sambaqui and Ribeirao da Ilha with low prevalence (3.3%); rickettsia-type bacteria, with greater prevalence in C. gigas (30%) than in C. rhizophorae , causing alteration in the epithelium of the stomach. It was not detected the presence of Perkinsus in any oyster sample analyzed of any site. Ciliates of genus Trichodina were observed among gill lamellae, digestive tubules, and adhered to the gills of oysters from Ribeirao da Ilha, with higher prevalence in C. rhizophorae (50%) and without causing injury. Protozoa Sphenophrya -type was found in the gills of C. gigas and C. rhizophorae , with higher prevalence in C. gigas from Sambaqui (70%), not causing changes in the gills. Protozoa of the genus Ancistrocoma were detected in the digestive tubules of C. gigas (36.7%) and C. rhizophorae (40%) from Sambaqui at low intensity and without causing apparent damage. Steinhausia -type microsporidians were observed in the cytoplasm of oocytes of C. rhizophorae and C. gigas with prevalences up to 33.3%. The intensity of infection in the animals was low, with only one oyster presenting more than 50 oocytes infected. The sporocysts of the pathogen caused alteration in the normal structure of the oocytes cytoplasm. Protozoa of genus Nematopsis were observed in the connective tissue of the gills and mantle with high prevalence (100%) in C. rhizophorae from Sambaqui, without host defense response. The observed metazoan were: turbellarians Urastoma -type, metacestode of genus Tylocephalum and copepods possibly of genus Pseudomiycola , all in low prevalence. None of the pathological occurrences found seems to cause significant damage in oysters, once they were found at low intensities. However, due to the great socioeconomic importance that the shellfish represent to the State of Santa Catarina, it's necessary to keep monitoring the health status of these populations.