Polygala fadimeana Dönmez and Çeçen is here described as a new species from the inner part of the Taurus mountain range in Turkey based on morphological data and its phylogenetic position is discussed based on molecular data. This new species is confined to limestone rock walls and is morphologically distinguished from P. kurdica and P. peshmenii by smaller plant size, nearly glabrous leaves, enrolled inner sepals, white colour crest, and other minor diagnostic features. However, a multi‐locus chloroplast phylogeny (trnL‐F and rbcL) including accessions of the new species and related taxa of Turkish Polygala revealed a close relationship to P. pruinosa and P. supina. The taxonomic relationship among the new species and P. kurdica, a poorly known species from Zagros Mountain range, and other closely related species such as P. pruinosa, P. peshmenii and P. supina are discussed. The new species is assessed as critically endangered (CR) based on current knowledge and the distribution of the new species and related taxa is mapped.