Hayachine-usuyukiso (Leontopodium hayachinense) is an alpine plant native to Mt Hayachine. This unique chrysanthemum is listed as an endangered plant by the Department of Conservation, Iwate Prefecture, and as a threatened plant by the Ministry of the Environment, Japan. We successfully cryopreserved the shoot tips from in vitro-grown L. hayachinense shoots using a vitrification protocol. Cold-hardened shoot tips were excised and pre-cultured on a solidified Murashige–Skoog medium containing 0.3 M sucrose for 1 d at 5°C. The shoot tips were then treated with loading solution for 20 min at 25°C, dehydrated in plant vitrification solution 2 for 120 min at 25°C and immersed in liquid nitrogen. The survival rate of the vitrified shoot tips was 63.3% after 30 d of regrowth. This protocol appears to be a promising technique for the cryopreservation of in vitro-grown shoots of this endangered plant.