Red mark syndrome (RMS) is a skin pathology affecting farmed rainbow trouts Oncorhynchus mykiss (Walbaum) that consists of bright red skin lesions on the flanks of the trunk of affected fish. The economical loss caused by RMS can be important. PCR and histopathological evidences indicate that this pathology could be caused by a single infectious agent, possibly a bacterium of the family Midichloriaceae (order Rickettsiales). Here we present a novel Real Time PCR method, useful to quantify the presence of this bacterium in fresh skin and organs but also in samples fixed on glass slides. The method was used to investigate the presence of the Midichloriaceae bacterium in samples from 14 fish individuals, obtained from three farms in Scotland. Positivity was obtained for all the examined skin lesions, but also for some samples of apparently healthy skin from affected fish, and from different organs of pathological fish. We were thus able to conclude that the hypothetical etiological agent of RMS is not only localized in the skin lesion, but can be detected in different organs of affected fish, suggesting a possible diffusion during the course of the pathology.