Major histocompatibility complex (MHC) class Ia genes in salmonid fishes are encoded by a single locus with probably the highest allelic diversity ever described. Various combinations of very different domain lineages contribute to the diversity of alleles. An extensive PCR survey distinguishing most domain lineages and their combinations was established. This survey has practical value for researchers investigating salmonid MHC class Ia variation. In the present study it was used to find new domain lineages. Applied for 24 hatchery strains in Japan, the survey identified two new rainbow trout alpha1 lineages and one new rainbow trout alpha2 lineage. The alpha2 lineage and one of the alpha1 lineages had been described in Atlantic salmon, but the other alpha1 lineage is novel. The newly identified trout alpha1 lineages are evolutionary very old. The present study should be the most extensive description of very deep MHC class Ia lineages to date: six trout alpha1 lineages cluster with non-salmonid sequences whereas previous studies mentioned this for only two salmonid alpha1 lineages. Although exon-shuffling events significantly contributed to salmonid MHC class Ia variation, analysis of 800 trout siblings did not detect such events within a single generation.