Two simple sequence repeats from chloroplast DNA (cpSSRs) and two mitochondrial DNA markers (rpl6-rps2 and trnW-trnI) were developed and used to investigate inheritance patterns of chloroplast and mitochondrial DNA in Saccharina japonica. Haplotypes were tested in 76 progeny sporophytes from two sets of reciprocal crosses between male and female gametophytes of S. japonica. The haplotypes were consistent with those of the maternal parents, proving that both the chloroplast and mitochondrial genomes were maternally inherited in all crosses. Forty-two cpSSRs and fourteen mtSSRs markers were developed for the present study, of which two cpSSRs and two mtSSRs proved to be polymorphic in 24 S. japonica individuals.