This study compared and contrasted the fate of the microsporidian Loma salmonae, a branchial pathogen of salmonids of the genus Oncorhynchus, upon exposure of (1) naive susceptible rainbow trout (RT) O. mykiss, (2) naive RT passively immunized with sera from RT previously exposed to L. salmonae, (3) previously exposed and resistant RT and (4) two species believed to be innately resistant to the parasite, Atlantic salmon (AS) Salmo salar and brook trout (BT) Salvelinus fontinalis. The fish were infected per os with viable L. salmonae spores. The infection was followed in the fish by detection of parasite DNA by polymerase chain reaction (PCR) at several times post‐infection. Spore germination and intestinal invasion by the parasite occurred in all groups of fish. In the susceptible RT, parasite DNA was detected in the heart by day 3 post‐exposure (PE), followed by the gill at 2 weeks PE, whereas visible xenoparasitic complexes (xenomas) were detected by week 4 PE. In the passively immunized RT, the parasite’s fate was similar to that of controls, however, its arrival in the heart was delayed by 1 week. A delay was also detected in RT which had been previously exposed to L. salmonae and then recovered from disease. In these resistant fish, the parasite was able to reach the heart by week 3 PE, however, it failed to reach the gill and form xenomas. In AS and BT, the parasite reached the heart and gills quickly, where it remained for 2 weeks before being cleared; xenomas never formed. We speculate that failure to complete the life cycle in AS, BT and resistant fish might be because of interference by the immune system in the development of the parasite, resulting in the absence of disease in these fish.