In the present research, we have investigated morphologicaltraits of different organs of Arabidopsis species in Iran. Trichomes on the aerial parts of three species were studied under anatomical microscopy. The species exist in Iran include: Arabidopsis thaliana (Heynh), Arabidopsis pumila (steph) and Arabidopsis wallichii (Hook & thomas). The form of trichomes, basal and stemleaves, fruit length, the attitude of fruit, the existence of trichomes on the fruit, and the color ofpetal are morphological traits which separate the species. Anatomical traits of the leaf and stem of studied species were analyzed using an optical microscope. In the stem, some traits such as the shape of stem in transverse incision, the thickness of skin, the existence of supporting tissue around phloem, the number of xylem and phloem and the wavy form of stele were distinct in the three species. In the leaf, some traits such as the shape of leaf, the number of palisade parenchyma layers, the uniformity of mesophyll tissue, and the density of trichomes were different in the three species. No significant difference has been observed in the study of reproductive meristem, except in A. wallichii. The only difference was related to the size of reproductive meristem of two species and the number of flowers produced from the meristems.