The invention provides a germplasm storage method for East Asian phyllitis japonica, which comprises the following steps that: prothallus is inoculated in a 1/4-MS (full) + sucrose 25-30 g/L medium, and the medium is placed in an illumination incubator, wherein the illumination intensity is 200-300 lx, the illumination is 5-7 h/d, and the temperature is 14-16 DEG C; 12 months later, almost no growth and proliferation occurs, and the state of the prothallus is similar as that in initial culture, and after the prothallus is transferred into successive culture conditions, the prothallus can proliferate and grow normally; and the prothallus is subjected to five-year storage treatment. The invention also provides an ex-situ conservation method for East Asian phyllitis japonica, which is implemented through a way that the stored prothallus is subjected to sub-cultured reproduction every year, and the formation and ex-situ transplanting of sporophore plants are induced by taking turfs as a matrix outside a test tube; three sits with basically similar as the original growing environment of phyllitis japonica are selected as ex-situ transplanting test areas in Changbai Mountains; 100 plants are planted at each site; and after growing 4 years, the growth vigour of the prothallus is good, thereby truly realizing the protection on endangered plants.