In this study, the phylogenetic relationship between some Dracocephalum species were investigated by Randomly Amplified Polymorphic DNA (RAPD) analysis, with total extracted DNAs. By thirty of 40 primers, polymorphic bands were observed. Genetic distances were calculated in order to construct phylogenetic dendrograms of closely related samples. Gas chromatography analysis supported the taxonomical classification. Based on the results the genetic distance between two samples of D. kotschyi was considered to be short and their RAPD banding patterns were quite similar to each other also there is a close relationship between two samples of D. arguense. Iranian samples of D. subcapitatum and D. kotschyi consist of limonene10al which could not be detected in Japanese samples of D. arguense so D. subcapitatum has very close relationship to D. kotschyi rather than D. arguense.