In Kazakhstan, the genus Tulipa is represented by 35 species, 18 of which are listed in the Red Data Book of Kazakhstan and protected by the state. Recent studies of tulip specimens from regions bordering Kazakhstan emphasize the significance of species inventory and report the discovery of several hybrids. In this study, eight tulip species were identified based on morphological characteristics and using DNA barcoding methods. Molecular genetic markers, including nrDNA (ITS) and cpDNA markers (rbcL, matK), of the studied species were sequenced and analyzed using the Bayesian inference and maximum likelihood phylogenetic analysis methods. Our work demonstrates that DNA barcodes based on the ITS, rbcL, and matK marker regions have successful practical applicability, with ITS being the most informative at the intragenic level. However, for distinguishing closely related taxa, the most effective approach would be to use a combined dataset of sequences from multiple DNA markers. The results showed discrepancies in the placement of several taxa (T. kaufmanniana, T. patens), likely due to introgression and natural spontaneous hybridization. The molecular phylogenetic analysis suggests the existence of a previously undescribed hybrid between T. patens and T. alberti. Further detailed population studies are needed to validate this hypothesis.

DNA barcoding is a reliable and effective tool for analyzing genetic and species diversity. Three plastid genetic markers (rbcL, psbA-trnH, matK) and one nuclear marker (ITS) were amplified with universal primers for species diversity and phylogenetic analysis of eight species including T. greigii, T. kaufmanniana, T. turkestanica, T. bifloriformis, T. patens, T. dubia, T. alberti, T. schrenkii across subgenera Tulipa and Eriostemones in Kazakhstan. DNA samples were obtained from fresh leaves of plants collected from various protected areas of Kazakhstan, and subsequently subjected to PCR, sequencing and deep phylogenetic analysis using Bayesian models for calculating posterior probabilities. Phylogenetic trees generated based on data obtained from individual markers accurately divided the samples into clades representing the subgenera Eriostemones and Tulipa. The ITS marker gave the most reliable results, followed by matK and rbcL; psbA-trnH was the least informative. These finding highlight the importance of using DNA-barcoding markers for comprehensive phylogenetic analysis, and contribute to understanding the genetic diversity and conservation of the Tulipa genus in Kazakhstan.