This paper includes the morphological and anatomical characters of the nutlets of 7 endemic species of the subsection Fragiles of the genus Stachys (Lamiaceae) from Turkey and the systematic significance of these characteristics, using one-way analysis of variance and cluster and principal component analyses. Morphological characters such as the dimensions, shapes, colors, and surfaces of the nutlets were studied using light and scanning electron microscopes. The structures and thicknesses of the pericarp and endosperm layers, as well as the sizes of the cotyledon in the nutlets, were anatomically studied. The outcomes revealed that the taxa vary from each other in terms of nutlet shape and color. The nutlet dimensions range from 1.31 mm to 3.49 mm in length and from 0.84 mm to 1.95 mm in width. While Stachys longiflora and S. pseudopinardii have the largest nutlets, S. chasmosericea has the smallest. The nutlet surface ornamentation was recorded as 5 types: reticulate, scalariform, reticulate-foveate, ruminate, and rugose. The most common type is reticulate; however, the other ornamentation types are specific for the studied taxa. Anatomically, the structure and thickness of the pericarp parts and the endosperm and the size of the cotyledon are very important characteristics that disclose interspecific relations within the studied taxa. A key is presented for the identification of the examined taxa based on the nutlet properties.