Achillea L. is a major genus in tribe Anthemideae of the family Asteraceae. In Egypt, the genus is represented by two species; Achillea fragrantissima (Forssk.) Sch. Bip and Achillea santolina L. Samples of 29 populations of A. fragrantissima and A. santolina L. were collected from their natural habitats as mature flowering plants, through 2009 to 2012, from different localities in Egypt. The relationship among the examined populations of Ac. fragrantissima and Ac. santolina was estimated based on variations in morphological traits and cytological features and polymorphism in molecular finger-printting separately and in combinations. The clustering of populations showed distinct grouping of populations from the same geographical regions together. In general, Ac. fragrantissima populations have relatively higher genetic diversity in comparisons of those of Ac. santolina.