| Summary: | Some wild, morphologically diverse taxa of the genus <i>Iris</i> in the broad Alpine-Dinaric area have never been explored molecularly, and/or have ambiguous systematic status. The main aims of our research were to perform a molecular study of critical <i>Iris</i> taxa from that area (especially a narrow endemic accepted species <i>I. adriatica</i>, for which we also analysed genome size) and to explore the contribution of eight microsatellites and highly variable chloroplast DNA (<i>ndhJ</i>, <i>rpoC1</i>) markers to the understanding of the <i>Iris</i> taxa taxonomy and phylogeny. Both the microsatellite-based UPGMA and plastid markers-based maximum likelihood analysis discriminated three main clusters in the set of 32 analysed samples, which correspond well to the lower taxonomic categories of the genus, and support separate status of ambiguous regional taxa (e.g., <i>I. sibirica</i> subsp. <i>erirrhiza</i>, <i>I.</i> x <i>croatica</i> and <i>I.</i> x <i>rotschildii</i>). The first molecular data on <i>I. adriatica</i> revealed its genome size (2C = 12.639 ± 0.202 pg) and indicated the existence of ecotypes. For future molecular characterisation of the genus we recommend the utilisation of microsatellite markers supplemented with a combination of plastid markers.
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