In the article, the results of studying the gene pools of the Kazakhstan coenopopulations of a rare plant species Pulsatilla patens (L.) Mill. are shown. The biomaterial taken from five coenopopulations located in Northern Kazakhstan has been used as samples. To identify the multilocus DNA polymorphism, the authors have used ISSR (Inter Simple Sequence Repeats, or intermicrosatellite analysis) labeling. The most effective primers have been selected, which provide reproducible results with a length of 17-19 nucleotides. As a result, multiple genomic labeling of five Pulsatilla patens coenopopulations has been performed. The main indicators of genetic diversity (P95 -0.965, HE -0.162, I -0.373 for the total sample), the structure and differentiation of the populations (HT -0.232, HS -0.162, GST -0.3 for the total sample) and the type and state of the gene pools of the studied coenopopulations have been determined. The specificity of the gene pools has been characterized by the number of rare alleles and the Coefficient of Genetic Originality (CGO). The maximum value of CGO has been noted at Pp5 (2.964) and the minimum one -at Pp4 (2.666). The gene pools of the Pp1 and Pp4 coenopopulations have been characterized as typical and gene pools of the Pp2, Pp3 and Pp5 -as specific. Based on the obtained data, tree diagrams have been made that reflect the degree of similarity of the studied coenopopulations as to the ISSR spectra. Identification of the state of the gene pools of rare plant species will allow recommending scientifically based measures for preserving them.