The genetic variation in four populations of Adenophora lilifolia (L.) DC., a rare plant species of the Perm region, was analyzed using 56 ISSR markers. The characteristics of DNA polymorphism and population genetic diversity were determined. These data demonstrate a high level of DNA polymorphism (P95 = 82.14%). The studied A. lilifolia populations are weakly differentiated; the intrapopulation variation is the main contributor to the genetic variation.