Eosinophilic Rickettsia-like organisms (E-RLO) were found for the first time in sick oysters of the species Crassostrea gigas, grown in Laguna de San Ignacio, Baja California Sur, Mexico, in August 2014. This work presents the histological description of development of bacteria in parasitophorous vacuoles of infected cells. Confirmative diagnosis was performed by polymerase chain reaction and in situ hybridization. Bacterial growth started with eosinophilic granules (colonial), followed by the formation and growth of intracytoplasmic inclusions. The presence of E-RLO was detected in the gill epithelium, mantle, labial palps, digestive tract, and both male and female gametes. This work describes for the first time an E-RLO in C. gigas with potential vertical transmission.