Genetic diversity and relationship of Fritillaria thunbergii Miq. landraces and related taxa

► High genetic diversity of F. thunbergii was revealed by ISSR marker. ► High genetic differentiation and relatively lower diversity were detected for the landraces. ► Kuanye (Ft-KY) landrace was relatively far away from other F. thunbergii landraces. ► Substantial genetic divergence occurred among the three species of Fritillaria. ► Genetic relationship between F. cirrhosa and F. anhuiensis is relatively close.