Infection patterns with ectoparasitic flagellates belonging to the genus Ichthyobodo were studied in an Atlantic salmon Salmo salar (L.) hatchery in western Norway during an 11 mo period, from eyed eggs to smoltification. Since the earlier species designation Ichthyobodo necator (sensu lato, s.l.) has been shown to represent a complex of several species, the epizootiology of different Ichthyobodo spp. is poorly known. Therefore, we employed molecular methods to ascertain the specific identity of the parasites detected in our study. Only I. necator in the recently redefined and restricted sense occurred (I. necator sensu stricto, s.s.). We observed a 2-peak pattern of infection; the first peak occurred among fry in March and the second peak among fingerlings and pre-smolt in August and September. Skin lesions observed on fingerlings and pre-smolt were significantly associated with Ichthyobodo infections. Also, these infections were negatively correlated with both haematocrit values (Hct) and the condition factor (K) of the fish. The patterns of infection on the farmed salmon suggest that I. necator s.s. is an opportunistic parasite of salmon, flourishing in periods when susceptible hosts are present and the environment favours parasite proliferation. Our study is the first to detect and identify I. necator s.s. on wild-caught adult salmonids (brown trout S. trutta L.). Wild salmonids and sticklebacks Gasterosteus aculeatus (L.) caught in the lakes serving as a water supply to the hatchery were found infected with I. necator s.s., hence these are the likely sources of parasites entering the hatchery via the inlet water.