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Background Fruit morphological characters have contributing useful taxonomic data and thus used to discriminate the species in different taxonomic rank. The fruit and seed morphology and anatomy in the family Ranunculaceae has been a long history and proved to be a great value for its phylogeny. Methods Achene morphology and pericarp anatomy of 12 taxa representing three genera (Anemone, Hepatica, and Pulsatilla) of tribe Anemoninae were investigated using microtome and light microscopy (LM) to evaluate taxonomic implications of achene characters. Results The achenes of Anemone were elliptical or obovoid and beaked, whereas the achene of Hepatica and Pulsatilla were obovoid and elliptical, respectively. Noticeable variations in both quantitative and qualitative features of achenes were observed among the species of three genera. One-way ANOVA indicated that the quantitative achene variables among the species were highly significant (P < 0.001). Pearson’s correlation coefficient also showed a significant correlation between different achene variables. The pericarp structure, particularly the number of cell layers and cell form in exocarp and endocarp seems to very useful for species delimitation in Amenome and Hepatica. The nature of endotesta could provide a substantial proof for sub-generic classification in Anemone. The UPGMA analysis also showed the utility of achene features for taxonomic groupings of the species within studied genera. Conclusion Although the sampling specimens represented a limited range of taxa the achene features and pericarp anatomy provide a reasonable source for the taxonomic treatment of studied genera within the tribe.