A major limiting factor in understanding teleost major histocompatibility receptor function is the lack of knowledge about antigen presentation accessory molecules. We report here two cDNA clones encoding teleost versions of invariant chain and one encoding a related protein that may play a protease inhibition role in antigen presentation. The two invariant chain equivalents are similar to each other where they overlap, but differ in the presence or absence of a thyroglobulin domain. This domain is added to tetrapod invariant chain protein by alternative splicing but there was no evidence of alternative splicing of the two trout genes. Southern blotting confirmed that all three trout cDNAs are derived from single copy genes and Northern blotting indicated that they are expressed in antigen tissues. Thus the encoded proteins are probably involved in antigen presentation, but their expression is probably regulated in a manner different from tetrapods.