A unique heavy chain of immunoglobulin (Ig) T was cloned from ayu Plecoglossus altivelis, and its in vivo expression was compared with IgM and IgD expression using quantitative RT-PCR and in situ hybridization. Three immunoglobulin domains, corresponding to C(H)1, C(H)2, and C(H)4, in IgT of other teleost fish species were conserved in the heavy chain. IgT mRNA levels were higher in the spleen, head kidney, trunk kidney, and gill tissue than in the intestine, liver, and skin tissue. IgM transcripts were the most abundant transcripts in all tissues tested. In the in situ hybridization studies, IgT and IgM mRNA-positive cells were scattered across the trunk kidney of healthy fish, while IgD mRNA-positive cells were not detected. mRNA levels of IgT and IgM were significantly upregulated in the gills and trunk kidney after vaccination with Vibrio anguillarum bacterin, but the IgD mRNA level remained unchanged. These results suggest that this unique IgT is expressed in a small number of cells and that it plays a role in immune responses induced by immersion vaccination.