Ballota undulate (rare), B. Saxatilis (endangered), and B. Kaiseri (extremely endangered and endemic) are three of Mediterranean origin species grow in southern Sinai Mountains. They are very close morphologically and have been confused and mixed in their natural habitats. The present study aimed to provide genetical and morphological differentiation among the three Ballotas peceis using allozyme, PCA, and discriminant analyses for plants growing in a common environment. Electroporetic analysis of enzymes coded by 21 gene loci demonstrated that there is a high degree of genetic similarity among the three Ballota species suggesting that speciation apparently has occurred in this genus with little divergence at genes coding for allozymes. Twelve quantitative and nine qualitative characters were selected for the study of phenotypic similarity and morphological variation in a sample of 147 plants, served as OUT's. The analyses could differentiate between B. undulata as one group and B. kaiseri and B. saxatilis as another group, but could not separate B. saxatilis from B. kaiseri. The incomplete isolation of B. undulata, B. kaiseri, and B. saxatilis, in combination with their high genetic identities and their very similar morphology, raise the question as to whether they should be retained as separate species.