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Chamomile (Matricaria chamomilla L.) is one of the most important medicinal plants in the world for many applications. In order to evaluate the genetic diversity of chamomile native populations based on morphological markers, 4 native chamomile populations including word, Jam and Riz, Hamedan and Buna cultivar were cultivated in a randomized complete block design with three replications. The traits of flower diameter, plant height and amount Harvest index and phenotypic variation coefficient of these traits were studied. The studied traits were analyzed by variance analysis and Duncan method was used at a significant level of 5%. The results of analysis of variance for height traits showed a significant difference at a probability level of 1%, but chamomites had no significant difference for flowering diameter, which indicates that the phenotypic variation coefficient (11.26) is very low. The highest altitudes for the Hamedan and Buna populations were respectively 80.06 and 78.53, respectively. Harvest index was significant as a key feature among the cultivars. The highest amount of altitude associated with Buna and Hamedan showed the highest harvest index (32.94) in Buna, which indicates the capacity of native populations to improve these traits.