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The present study was aimed to investigate foliar anatomy and flower, fruit and seed morphology of three subspecies of Agrimonia eupatoria (i.e. A. eupatoria subsp. eupatoria, A. eupatoria subsp. grandis and A. eupatoria subsp. asiatica) and the species of Aremonia agrimonioides, belonging to the subtribe Agrimoniiae (Rosaceae) in Iran. Firstly, plant specimens were collected and then identified on the basis of relevant references. For anatomical analysis, the cross sections of basal leaves of each taxon were prepared, studied by light microscopy and then photographed by means of a digital camera. For morphological analysis, the flower, achene and seed characters were carefully examined using digital microscopy. To determine the relationships among the taxa, 57 characters were included in the Principal Component Analysis (PCA). The results supported the classification proposed by Flora Iranica and showed the importance of leaf anatomical, flower, achene and seed morphological characters in separating inter-generic, intraspecific and interspecific relationships among the representatives of subtribe Agrimoniinea in Iran.