The novel, phylogeny-based classification of Iris s.l. in the Mountains of Central Asia biodiversity hotspot has been developed. Fifty seven species are accepted and classified into 14 sections. The majority of accepted species (38) belong to the juno irises, which have a centre of their diversity in Central Asia and are represented by 2 sections; the largest I. sect. Juno is subdivided into 10 species groups, whereas I. sect. Physocaulon is subdivided into 2 subsections, each with 2 aggregates. The analysis of the geographical pattern of species richness revealed two areas of exceptionally high Iris species richness: Tian-Shan (14 species) and Hissar Mts. (21 species). A morphological description, sample photograph, geographical distribution, ecological data, point distribution maps, list of specimens and photographs examined, synonymy and nomenclatural type are provided for each species. A new identification key is compiled, based on morphology and phylogenetic relationships. Iris alberti Regel is reported for the first time from Uzbekistan. Four new combinations, Iris sect. Sclerosiphon (Nevski) Sennikov & F.O.Khass., I. subsect. Drepanophyllae (Rodion.) Sennikov, I. subsect. Rosenbachianae (Rodion.) Sennikov and I. parvula (Vved.) Sennikov, are established. The name I. kopetdagensis Vved. is validated with a type and description in English. Iris suworowii Regel is restored as the priority name for I. lineata Foster. Iris popovii Vved. is treated as a synonym of I. baldshuanica O.Fedtsch. & B.Fedtsch., I. pskemensis Rukšāns as a synonym of I. kolpakowskiana Regel, I. hoogiana Dykes as a synonym of I. darwasica Regel, and Iridodictyum kopetdaghense Kurbanov is reduced to a synonym of Iris reticulata M.Bieb. Iris almaatensis Pavlov is removed from synonyms of I. subdecolorata Vved. and considered a yellow form of I. kuschakewiczii B.Fedtsch. The nomenclature of I. sect. Regelia (Foster) Foster, I. parvula (Vved.) Sennikov and I. sogdiana Bunge is corrected. The names I. sect. Regelia (Foster) Foster, I. alberti Regel, I. bloudowii Ledeb., I. halophila Pall., I. hoogiana Dykes, I. lineata Foster, I. regelii Maxim. ex Regel, I. scariosa Willd. ex Link, I. sogdiana Bunge, I. stolonifera Maxim., I. suworowii Regel, I. tenuifolia Pall., I. tenuifolia var. thianschanica Maxim. ex Regel and I. vaga Foster are lectotypified, whereas I. suworowii is also epitypified.