Polymerase chain reaction(PGR)-based inter-simple sequence repeats(I-SSR) markers were analyzed in 48 megagametophytes of a single tree of Abies koreana W_(ILS). Nineteen of the 35 primers, screened with 6 megagametophyte DNA and produced the clearest amplification products in the preliminary experiment, were used for PCR with 48 megagametophyte DNAs sampled from a single tree. On the basis of the chi-square test, a total of 51 amplicons, amplified by the 19 primers, were revealed to be segregated according to the Mendelian ratio(i.e., 1 : 1 segregation ratio) in the 48 megagametophytes at 5% significance level. Based on the linkage analysis, the observed 51 Mendelian loci turned out to be unlinked each other, which suggested that they are evenly distributed in the genome. However, majority of RAPD markers are known to belong to the independent linkage blocks, which frequently results in the amplification of RAPD markers from the restricted regions of the genome. Owing to the nature of even distribution of the 51 loci observed in this study, the I-SSR markers could give better resolution of estimating genetic diversity from the whole genome than RAPD markers. And I-SSR markers are also more suitable than RAPD markers for reconstructing phylogenetic relationship by a cladistic method which requires to fulfil the assumption of independent evolution of the different characters.