Anatomical and morphological seed traits are of great ecological importance and are a main subject of, for example, seed bank or endozoochory studies. However, we observed a lack of information about the relationship between seed anatomy and seed morphology and its ecological implications. To fill this gap, we linked the anatomical features of diaspore coverings to morphological characteristics of free seeds and one-seeded fruits. We predicted that: (1) the thickness and anatomical complexity of seed coat and pericarp are related to diaspore size and shape; and (2) the presence or absence of the pericarp may influence seed-coat thickness and anatomy. In our study we investigated diaspores of 39 central-eastern European herbaceous species and recorded the thickness and anatomical complexity of their seed coverings, and we determined diaspore mass and shape. Our results indicate that diaspore mass is positively related to covering thickness, lignification degree and anatomical complexity. This might be the case because bigger diaspores tend to remain on the soil surface and are more exposed to predation risk and environmental threat than smaller diaspores. Furthermore, more round-shaped diaspores had disproportionately thicker and more lignified coverings than long or flat ones, probably because round-shaped diaspores much more frequently form seed banks and therefore persist for a long time in the soil. We also found that free seeds as diaspores have a thicker and more lignified seed coat than seeds enclosed in fruits. In one-seeded fruits, the pericarp ‘takes the protective role’, it is thick, and the seed coat is poorly developed.