As part of our ongoing studies, a new and validated method for analysis of isohexenyl-naphthazarines in Turkish Alkanna species was developed. By using reversed phase material (Synergi MAX RP) it was possible to determine four known isohexenylnaphthazarin-derivatives, namely alkannin, acetylalkannin, deoxyalkannin, and beta,beta-dimethylacrylalkannin within 25 min in n-hexane extracts of the roots. The quantification of these compounds in 16 Anatolian Alkanna species is described for the first time. In order to assure peak identity LC-MS experiments were performed. Quantitative results revealed that the most dominant compound in the extracts was beta,beta-dimethylacrylalkannin.