We evaluated the morphological characteristics of 54 Perilla accessions by examining two quantitative and four qualitative characteristics in order to understand better the relationships between the cultivated types and the weedy types of Perilla species. The size, germination rate, hardness, and color of seeds were examined. The cultivated type of Perilla frutescens var. frutescens showed variation in seed size (2.08 to 2.96 mm) and germination rate (54 to 99%). Most accessions had soft seeds, but the seed colors of white, gray, brown, and dark brown. The weedy type of var. frutescens also showed the variation in seed size (1.54 to 1.94 mm), germination rate (0 to 46%), and had only the hard seeds in dark brown. The cultivated type of var. crispa showed the seed size range of 1.6 to 1.72 mm, and the germination rate of 3 to 34%, and had only the hard seeds in dark brown. The weedy type of var. crispa showed the seed size of 1.45 to 1.96 mm, the germination rate of 0 to 27%, and also hard seeds with dark brown color. The accessions of cultivated type of var. frutescens exhibited the bigger variation in seed characteristics than the weedy type of var. frutescens and the cultivated and weedy types of var. crispa. Principal component analyses clearly discriminated between the cultivated and weedy types in var. frutescens, and between var. frutescens and var. crispa in the two cultivated types. However, the seed characteristics of the cultivated type and the weedy type in var. crispa were not clearly discriminated. In this study, the size, germination rate, and hardness of seed were the useful characters for discriminating var. frutescens and var. crispa in the cultivated types, and the cultivated type and the weedy type in var. frutescens. The cultivated type of var. frutescens might be regarded as a more domesticated type than the cultivated type of var. crispa.