In order to provide reliable theoretical basis for high-efficiency utilization of Saccharina japonica germplasm resources in its breeding practice, the information of genetic diversity and structure of three new edible S. japonica cultivars (including “Haitian No.1”, “Haitian No.2” and “Haitian No.3”) and “Huangguan No.1” were explored in this study. We selected eight pairs of primers for the simple sequence repeat (SSR) molecular marker technique to test the genetic diversity of 120 samples of the four S. japonica cultivars. From 20 pairs of SSR primers published online, eight pairs were identified because of their good amplification patterns on the majority of 120 DNA templates. The results showed that 28 polymorphic alleles and 9 specific alleles were detected by eight SSR markers, and the average alleles per primers detected were about 4.6250. The Nei¢s gene diversity (H) and the Shannon index (I) of the four S. japonica cultivars were 0.3809 and 0.6702, respectively. It indicated that the genetic diversity of the four S.japonica was relatively low and four species were genetically related. Among them, the Nei¢s gene diversity (H), Shannon¢s information index (I) and the number of polymorphic alleles were the highest in “Haitian No.1”. This indicated that the genetic diversity of S. japonica of “Haitian No.1” was higher than other three S. japonica cultivars. The levels of genetic diversity of “Haitian No.2”、“Haitian No.3” and “Huangguan No.1” decreased successively. Cluster analysis demonstrated that the relationship between “Haitian No.1” and “Haitian No.3” was close, but the relationship between “Haitian No.1” and “Huangguan No.1” was not. AMOVA analysis showed that about 92.06% of the variation was derived from individuals of the four S. japonica cultivars, and 7.94% of the variation was derived among the four S. japonica cultivars. The genetic diversity of “Huangguan No.1” was the lowest, suggesting the need of strengthening the biodiversity protection; the highest genetic diversity was the “Haitian No.1”, and could be used for developing new cultivars.