Genetic and phytochemical diversities of Cynomorium songaricum Rupr. in Northwest China indicated by ISSR markers and HPLC-fingerprinting

► Genetic and phytochemical diversities of Cynomorium songaricum Rupr. were analyzed. ► Dendrogram based on genetic distance showed the origin pattern of C. songaricum. ► Dendrogram of HPLC-fingerprinting was related with geographic environment. ► Total phenolic acids content was ranging from 56.79 to 123.50 mg g−1 ► A planting and conservation system of C. songaricum was suggested in this study.