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Iris is a cosmopolitan genus comprising 200 to 340 species distributed throughout the Northern Hemisphere. Although Iris is the most diverse group in the family Iridaceae, there are many uncertainties regarding its taxonomic composition and systematics. The aim of this study was to search for taxonomically significant morphological characters of the generative and vegetative spheres and molecular markers with subsequent assessment of their informativeness in identifying phylogenetic relationships and compliance with the most relevant modern classification systems of the genus Iris. As a result of constructing the structure of variability of morphometric parameters of 11 species, 10 taxonomic indicators were identified that were common to the analyzed taxa and were characterized by relatively low total and coordinated variability: length and width of the outer perianth lobes, length and width of the inner perianth lobes, length of the filament, anther and pistil, fruit width, as well as seed length and width. Nucleotide sequences of trnL-trnF fragments of chloroplast DNA were established for 13 samples of four species of wild flora of the Republic of Bashkortostan and the Orenburg Region: Iris pumila L., I. scariosa Willd. ex Link., I. pseudacorus L., I. sibirica L. The obtained sequences were used to construct a phylogenetic tree together with trnL-trnF sequences of seven more iris species extracted from the database. The tree contained five clusters: (1) I. pumila, I. scariosa; (2) I. pseudacorus, I. setosa Pall. ex Link; (3) I. lactea Pall.; (4) I. sibirica, I. sanguinea Hornem.; (5) I. spuria L., I. xanthospuria Mathew & Baytop., I. foetidissima L., I. sintenisii Janka. By the composition of their species, the identified clusters almost completely coincided with the clusters found during the morphological analysis. To confirm the obtained results, a phylogenetic analysis of the species of interest was performed on two more chloroplast sequences available in the database: matK and trnS-trnG. Clustering of the studied species on trnS-trnG and matK completely coincided with clustering on trnL-trnF. Thus, we can state that the morphological features identified for the Iris generic complex work in the taxonomic direction. The analysis also showed that I. scariosa from natural populations of the Republic of Bashkortostan and the Orenburg Region were identified correctly.