ABSTRACT.    Members of the family Francisellaceae (Gammaproteobacteria) are short rod-shaped or coccoid facultative intracellular bacteria. The genus Francisella comprehends two species, F. tularensis and F. philomiragia. F. tularensis is the etiological agent of tularaemia. Human tularaemia is a febrile, zoonotic disease, transmitted by direct contact with infected animals, through contaminated water or food, or by vectors such as biting insects or ticks. The second species, F. philomiragia, is less virulent and is often closely linked to water-borne transmission. It may cause severe disease with pneumonia and/or septicaemia. The majority of cases has occurred in immunocompromised individuals or near-drowning patients. In the present study, intracellular bacteria were detected in the marine ciliate Euplotes raikovi strain 1 by screening with Fluorescence in situ Hybridization (FISH) using a universal probe. These bacteria were characterized by the full cycle rRNA approach. PCR amplification, cloning and sequencing revealed the presence of bacteria closely related to Francisella. To complete the full cycle rRNA approach, FISH experiments with a Francisella-specific probe were performed and they confirmed the presence of Francisella-like bacteria within the Euplotes cells. Phylogenetic analyses showed that the intracellular bacteria of E. raikovi strain 1 belong to a branch that includes F. philomiragia. Hitherto these bacteria have been found only as endosymbionts in arthropods, or as intracellular pathogens in rodents, but never in protists. This finding raises the question if protists serve as a natural reservoir for infective bacteria in a much larger extent than previously expected. Moreover, it reveals the need of further investigations on possible new routes of infection and transmission of these bacteria, especially regarding human diseases.