There are two taxonomic varieties of spinach (Spinacia oleracea L.), the spiny variety [S. oleracea var. spinosa (Moench)] and the spineless variety [S. oleracea var. inermis (Moench) Peterm.], based on the spines of spinach fruits. Between the two varieties, there are obvious differences in the leathery fruit coat but no significant differences in the macro-morphological appearance of seeds. Differences between the two varieties are hard to see without the fruit coat, which makes seed purity analysis difficult. In this study, the morphological structures of fruits and seeds from 31 spinach cultivars were compared. The results showed that there were significant differences in the macro-morphology of spinach fruit in terms of fruit shapes and the presence of spines, but no significant differences in the micro-morphology of the fruit surface under a scanning electron microscope (SEM) between the spineless and spiny varieties. In addition, there were no clear and stable differences between the two varieties in seed macro-morphology based on stereomicroscopy, or in the internal seed structure based on micro-computed tomography imaging. However, significant differences in seed micro-morphology could be observed under SEM, particularly for the surface reticulation of the seed coat, such as the depth of interspaces, sidewall angle, and the bottoms of interspaces. The differences in seed micro-morphology allowed for clear discrimination between the two varieties. These results provide morphological evidence for distinguishing fruits and seeds between the two spinach taxonomic varieties, and these similarities and differences can be used to classify spinach cultivars and to analyze seed purity.