We aimed to analyse the seed coat of Glycine species accessions, in particular, the morphology and fine structure, by scanning electron microscopy. The seed coat makes up about 6.7% and 22.9% of the seed weight in the Glycine max cv. Shishi and Glycine soja, respectively, and 30% to 40% in other species (Glycine canesences, Glycine latifolia, Glycine tabacina, Glycine tomentella) surveyed in this study. The seed coat surface of the cultivar contained pores and deposits, and the bloom formed by these deposits coming from the endocarp was present in all of the species examined except the cultivar Shishi. As well, the cavity sizes of the bloom were significantly different among these accessions. These characters, including seed weight, seed length, seed coat proportion and cavity density, might be helpful in Glycine species taxonomy.