Seed and leaves for 11 taxa represented by three genera of Zygophyllaceae are examined by scanning electron microscope to investigate the different characters which can be used for identification and differentiation between them. The morphology of seed for the studied taxa has different characters in color, size, hilum position and shape. Seed coat sculpture recorded eight pattern of seed coat. The characters of epidermis are different for stomata, cuticular ornamentation and trichomes types. The studied taxa recorded 16 types of trichomes, 4 glandular & 12 non-glandular and 5types of cuticular ornamentation. A bracketed key is provided for differentiation and identification between the investigated taxa. All characters from seed coat sculpture and epidermis were used for numerical analysis. The results showed that studied taxa were classified into two major clusters, the first (I) consisting of the four taxa of Tribulus, while the second cluster (II) comprises the studied taxa of Fagonia and Tetraena.