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Glycyrrhiza uralensis is an endangered and national-protected medicinal plant species distributed in semi-arid and arid areas of North China. This study addresses the genetic diversity and relationship between populations in different habitats by amplified fragment length polymorphism (AFLP). The plant materials consisted of 50 individuals from 5 different populating areas of Chifeng (Inner Mongolia), Hengjinqi (Inner Mongolia), Minqin (Ganshu), Aletai (Xinjiang) and Kashi (Xinjiang). Eight AFLP primer combinations generated a total of 1025 bands with 52.7% polymorphism. Unweighted pair group method based on arithmetic average (UPGMA) analysis was performed on Jaccard’s similarity coefficient matrix. According to results, the genetic resources and diversity in wild populations of G. uralensis were rich (polymorphism = 54.3%, He = 0.1932). The polymorphism among populations was Chifeng > Hangjinqi > Minqin > Aletai > Kashi and the genetic diversity varied from 0.1794 - 0.2061 and was in the order of Minqin > Chifeng > Hangjinqi > Aletai > Kashi. Genetic diversity was significantly correlated with annual mean precipitation and soil pH. Aletai and Kashi populations had close genetic relationship, and so Minqin and Chifeng populations. Conservational efforts have to be strengthened for all populations of the plant species in different habitats.