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Substantial differences occur between the male and female gametophytes of Laminaria japonica Aresch in morphology and physiology. The differences were investigated by screening a cDNA library generated by suppression subtractive hybridization (SSH). Using bioinformatics and northern blot analysis, we confirmed that two genes, lhcf6 and fcp, were preferentially expressed in male gametophytes. Analyses of the randomly selected 627 clones generated by this cDNA library showed that 9 of them were unreadable due to low quality. The remainders were assembled into 187 non-redundant sequences (NRSs), of which 93 Contigs were from 524 cDNAs, showing that the redundancy rate was 69.74%. Among the 187 NRSs, 60 NRSs matched homologous proteins in public database while 122 NRSs had no significant similarity regardless of 5 NRSs due to their contamination of rRNA genes. Many of the NRSs were involved in growth and development (13.3%) and metabolism of energy and substances (26.7%) of gametophytes. In the case of metabolism, 106 cDNAs are components of the light-harvesting complex proteins, in which lhcf6 was composed of 62 NRSs and fcp was of 12 NRSs. These results showed that SSH was a useful method for discovering the differentially expressed genes between male and female gametophytes of L. japonica and for functional genomics research in this kelp. Keywords-Laminaria japonica Aresch., gametophytes, SSH, cDNA library, differentially expressed gene