Microsatellite DNA (SSR) Marker was used to identify both conchocelis and gametophytic blades of the SF-2 strain of conchocelis DNA of the SF-2 strain, which was significantly differentand also presented in the gametophytic blades of the SF-2 straincultured in the laboratory. When the primer-pair was applied to discriminate SF-2 cultivation ground, the SSR marker showed the same results blades cultured at different cultivation grounds or harvested at different times. Analysis on DNA sequences of the specific bands showed that the SSR markers amplified by 9# primer-pair reflected the changes of simple sequence repeats. Respected motif sequences had been searched out by the software of SSR Hunter and the products were within the prospective lengths when the primer-pair was designed. The sequence turned out to be a new sequence because no similar sequence was found in the NCBI nucleic acid database by BLAST. Analysis of sequences by DNAMAN software showed that there were fewer differences between “SF-2” and “SF-1” but more differences compared to “WT-xp” cultivated in Xiapu, Fujian Province. Therefore, it was confirmedthat the SSR marker reflected the differences between strains and could be used to identify intra-specific strains. All the above showed that the specific primer-pair was the specific SSR marker in both conchocelis and gametophytic blades of the SF-2 strain and could be used to identify the SF-2strain from the current cultivars