Oxytropis glandulosa Turcz. (Fabaceae) is a rare perennial plant endemic to Buryatia (Russia). We sequenced three intergenic spacers (the psbA−trnH, trnL−trnF, and trnS−trnG) of chloroplast DNA (cpDNA) in specimens of four populations from two geographic regions (Barguzin and Yeravna depressions) within this species range. The levels of haplotype and nucleotide diversity varied in the range of 0.133−0.911 and 0.0002−0.0059, respectively. The highest values of these parameters are characteristic of populations located in the Barguzin depression. Variable sites detected within the intergenic spacers allowed the identification of eleven haplotypes; nine of them were found in the populations from the Barguzin depression and only two haplotypes were found in the populations from the Yeravna depression. No common haplotypes for all four populations were found. A high level of population differentiation (ΦST = 0.758, P < 0.0001) and the absence of evidence for isolation by distance were also found in O. glandulosa. Genealogical and phylogenetic analyses and Bayesian analysis of the genetic structure showed a clear division of the studied populations of O. glandulosa into three major lineages.