We tested the phylogenetic utility of three chloroplast DNA loci, i.e. the trnL(UAA) intron, trnL(UAA)-F(GAA) intergenic spacer (IGS), and trnV(UAC) intron, across thirteen native Oxytropis species. Our objective was to determine whether any of these chloroplast DNA markers could be beneficial to figure out phylogenetic relationships among Oxytropis species. To increase the interspecific sampling, nine sequences of the trnL intron and trnL-F regions were retrieved from GenBank and included in the analyses. No sequence of the trnV intron region was available in the database and so only sequences of the native species were used for the analyses. Phylogenies derived from maximum likelihood and maximum parsimony analyses indicated that the trnL intron and trnV intron regions provided better resolution for relationships among species with respect to the trnL-F region. The highest variable and parsimony informative sites were observed in the trnL intron region, while the lowest sites were seen in the trnV intron. Less variable sites for the trnV intron region were expected since no foreign sequences could be included in the analysis. Oxytropis lazica was phylogenetically separated from native species and clustered with foreign ones when the trnL intron and trnL-F regions were analyzed. The result obtained from the trnV intron region proved that Oxytropis engizekensis Duman and Vural may be a synonym of O. persica Boiss. A previous study that used morphological characters arrived at a similar conclusion.