Display omitted •Three stages of E-RLO infection were identified based on internal lesions.•The intensity of infection differed between tissues.•Damage suggests that the E-RLO has the capacity to impairs the C. gigas. Rickettsia infection in adult Japanese oysters (Crassostrea gigas) was observed in 2015 at San Ignacio Lagoon, Baja California Sur, Mexico and characterized using molecular tools. In the present study, the degree of infection by Eosinophilic Rickettsia-Like Organism (E-RLO), characterized by intracellular inclusions in gill, mantle, labial palps, digestive tract and gonadal ducts, was evaluated using histological methods and was associated with visible injuries on body surface, such as blisters, shell damage and necrosis. Most of the oysters (92.2%) had some type of observable symptoms; 90.2% of all oysters had blisters in the mantle, and all oysters presented with E-RLO in the epithelia of at least one of the analyzed tissues (gills, labial palps, mantle, gonadal ducts and digestive tract). The highest intensity of infection (percent of E-RLO coverage) was observed in the labial palps (18.6%) and the lowest in digestive tract (2.6% of the examined tissue). Oysters with external injuries had higher infection intensities than the oysters without external injuries. Considering the clinical signs (observable symptoms and histological findings), we propose three infective stages of E-RLO disease development, a scale that could be used for early detection.