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Fruit morphological and anatomical characteristics are essential in the taxonomy of Apiaceae. Daucus L. is one of the most important genera of the family Apiaceae, as it contains the cultivated carrot, a crop of great economic importance, and about 40 wild species that could serve as potential sources of genetic diversity for crop improvement. However, the taxonomic and phylogenetic relationships among these species have not yet been fully clarified. In this study, we comparatively investigated the fruit morphology and anatomy of 13 Daucus taxa and four closely related non-Daucus species using light and scanning electron microscopy to evaluate the taxonomic value of these characteristics. A wide range of variations was observed in the fruit morpho-anatomical characteristics across the taxa and revealed several diagnostically valuable features, thus proving to be taxonomically useful. For Daucus, the observed differences included the fruit size (2.1–8.4 mm), shape (from ellipsoid to oblong), and weight (0.079–1.349 g/100 fruits), as well as the fruit surface sculpturing and some anatomical characteristics, i.e., the presence/absence and size of vittae, the shape and size of vascular bundles, and the shape of exocarp cells. This study contributes to a better understanding of the relationships among the genus Daucus.