To investigate regulatory mechanisms of proopiomelanocortin (POMC) gene expression in sockeye salmon, we have isolated and characterized cDNAs encoding two types of sockeye salmon POMC, which are referred to as ssPOMC-A and -B. Two types of PCR products were amplified from total RNA of sockeye salmon pituitaries by use of rainbow trout sequences. Full length cDNA clones encoding ssPOMC-A and ssPOMC-B were obtained from a pituitary cDNA library of sockeye salmon using the PCR products as probes. The ssPOMC-A and -B cDNAs have a length of 1072 and 1709 bps, respectively. Northern blot analysis showed that both ssPOMC-A and -B mRNAs were expressed only in the pituitary, and their sizes were about 1.2 kb and 1.8 kb, respectively. The presence of two ssPOMC genes was confirmed by Southern blot analysis of genomic DNA obtained from a single sockeye salmon. The deduced amino acid sequences of the ssPOMC-A and -B contained 230 and 226 residues, respectively. The amino terminal of beta-endorphin in ssPOMC-B which corresponds to Met-enkephalin domain is YSGFM, which is different from YGGFM of Met-enkephalin found in many other vertebrate species. The homology of nucleotide sequences between ssPOMC-A and -B is 59% in the entire coding region, whereas alpha-MSH coding regions are highly homologous (91%). Although the deduced amino acid sequences of ssPOMCs show 43% overall similarity, their hydropathy profiles are coincident with those of several other vertebrate species, particularly the amino terminal of N-terminal peptide (NPP) shows almost the same pattern with other vertebrate NPPs.