Aim and Background. The two genera Chenopodium and Atriplex contain 100 and 150 species, respectively both of which belong to Chenopodiaceae family. Due to morphological similarity, the recognition of species of these two genera is comparatively difficult, thus, the anatomical characters are considered in the southern Khorasan Province.

Materials and Methods. At first, for studying anatomical structure of species, herbal samples were gathered from different areas of this province. Then, the method of manual cutting was used in laboratory, and for staining tissues and better distinguishing their organizing sections, the method of with green methyl and Carmen stain. After preparing slides, photo was provided for all sections (leaf, stem, petiole and epiderm) and anatomical characters were evaluated by Olympus microscope equipped with ruler.

Results. The results show the characters of leaf and stem were distinctive in genus, but they couldn’t distinguish the species of each genus. In the species of C. botrys glandular trichomes, to be thick of its coticule in both surfaces, the form of petiole section and type of stomata is below surface in both level of epiderm, to distinguish it from other species of Chenopodium genus.

Conclusions. The most differences have been seen in the petiole character signifying the recognition of the species.