Tulipa is a genus that comprises species highly valued as ornamentals throughout the world. So far, only a few Tulipa plastid genomes have been reported, and there are many taxonomically controversial species. In this study, we sequenced the chloroplast genomes (CP) of nineteen species collected from Uzbekistan and Kyrgyzstan and conducted comparative analysis. In all CP, 136 genes were annotated, of which 114 were unique, including 80 protein-coding, 30 tRNA, and 4 rRNA genes. Polymorphic SSRs effective for discrimination between species and populations were identified. Additionally, comparative Pi diversity analysis of both protein coding genes and whole plastomes revealed that the ndhE, ndhF, psaC, rpl32 and ycf1 genes and the regions rps16–trnQ-UUG, psbM–psbD, trnT-UGU–trnL-UAA, petA–psbJ, rpl33–rps18, petD–rpoA, rpl36–rpl14, rpl32–ccsA have higher variability than others. Further, phylogenetic reconstruction including 37 species of Tulipa and 3 outgroups based on 76 shared coding sequences (CDS) and ycf1 genes were made. Both phylogenetic trees divided the species into three major clades, and they had almost the same topology, confirming that ycf1can be used as a marker for phylogenetic relationships. However, the currently recognized sections appear non-monophyletic. Insights into the taxonomic classification of several species of Tulipa, based on several morphologic, phytogeographic, and molecular data are discussed.

The data was collected from herbarium, natural habitats and GBIF. Phylogenetic trees were built using MrBayes software.