The micromorphological traits of seeds (M. medicaginoides, M. monantha, M.orthocerac, M. monspeliaca, M. brachycarpa, M.radiata) of six Medicago L. species spread in Azerbaijan have been studied with stereo microscope and scanning electron microscope (SEM). The status of some species of Medicago genus included to Trigonellinae of Trifolieae tribe is controversial. During the observation, the difference between the quality and quantity parameters of those taxa was revealed. The seeds have been compared for its shape, color, hilum shape, position and surface patterns and etc. Their taxonomical significance have been discussed. The studied traits are significant in determination of systematical position and identification of species.