Species of the genus Ziziphora (Lamiaceae) are valuable medicinal and economically significant plants in the flora of Uzbekistan. Due to morphological similarities among species, accurate identification has been challenging. This study presents the first comprehensive analysis of the complete chloroplast genomes of species of Ziziphora native to Uzbekistan. Comparative analysis revealed genome size variation, conserved circular structures, and differences in nucleotide compositions. Each genome contains 131 genes, 86 of which are protein-coding and mainly associated with photosynthesis and plastid function. A relatively low GC (~37.8%) content is characteristic of chloroplast DNA compared to nuclear genomes of Ziziphora species. Phylogenetic analyses based on whole chloroplast genomes and selected variable markers positioned Ziziphora species as a distinct monophyletic lineage within the tribe Mentheae of the subfamily Nepetoideae. The results support the use of chloroplast DNA as a reliable marker in molecular phylogenetic taxonomy and evolutionary studies. This research contributes essential insights into the genetic structure, evolutionary history, and taxonomic placement of taxa of Ziziphora, providing a valuable foundation for conservation strategies.

Keywords: chloroplast genome, genetic structure, genome size variation, Lamiaceae, molecular taxonomy, phylogenetic analysis, taxonomic placement, Ziziphora

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