The first specimens of Allium elmaliense were collected in Elmal? (Antalya/Turkey) in 2001 and were described as new species in 2004. However, Allium elmaliense was claimed as synonym of Allium cyrilli in 2006. This study was undertaken to reveal the differences between these taxa utilizing morphological, palynological, and chromosome characters and genomic differences based on the DNA analyses along with the ecological preference studies conducted during 2006 and 2011. The results clearly indicated differences between these two taxa in terms of morphological characters, pollen, seed surfaces and niche preferences. Chromosome morphology and Td-DAMD-PCR fingerprinting studies revealed that Allium elmaliense Deniz & Sumbul is a distinct species and not a synonym of A. cyrilli Ten.