We studied morphological and anatomical characteristics of seeds of 22 taxa in the sections Nomisma, Thlaspi, and Pterotropis of Thlaspi sensu lato from Turkey and the significance of these characters in a taxonomical context. The results show that the taxa differ from each other in terms of seed shape and color. The seed size ranges from 1.25 mm to 2.99 mm in length and from 0.66 mm to 2.16 mm in width, Thlaspi rosulare and T tatianae having the largest and T annuum having the smallest seeds. The seed surface ornamentation is classified into nine types: reticulate-areolate, scalariform, reticulate, reticulate-foveate, ruminate, ocellate, tuberculate, areolate, and colliculate. The most common type is reticulate- areolate, whereas areolate, colliculate, ocellate, and tuberculate ornamentation types were found to be taxon-specific. The testa is typically made up of four layers: the epidermis, the subepidermis, the sclerotic (or palisade) layer, and the parenchyma layer. The sclerotic (or palisade) layer may not be seen in some of the species. The structures and thicknesses of the epidermis, the subepidermis, the sclerotic (or palisade) layer, and the parenchyma layer are highly significant characters that reveal interspecific relationships within the examined taxa. The results are also compared with Meyer's findings and classification of 1973, 1979, 1991, and 2001, and taxon transfers are questioned. In addition, a key is provided for the identification of the examined taxa based on seed characteristics.