Perilla is a self-fertilizing crop widely used in East Asia for its seeds and leaves. Of the two varieties of Perilla, P. frutescens var. frutescens has long been used as a folk plant in South Korea. The seeds are rich in unsaturated fatty acids, which offer significant health benefits, making them popular for use in seed oil or as a spice. The leaves, with their high perilla ketone content and unique aroma, are used as leafy vegetables and spices. The morphological characteristics of crops are complex for various reasons, such as environment factors, multiplicity, etc. To better understand the morphological variations among three types of Perilla collected from three regions of South Korea, 7 qualitative traits and 10 quantitative traits were investigated using 500 Perilla accessions. The results of principal component analysis (PCA) indicated that the first two components together explained 52.2% of the overall variation. The 500 Perilla accessions clearly distinguished cultivated var. frutescens from weedy var. crispa and also revealed differences between cultivated and weedy types of var. frutescens. Significant morphological differences were observed among the three types of Perilla, especially in seed and plant characteristics. When the PCA results were analysed by region, regional differences were observed for all three types of Perilla. Therefore, this study provides a better understanding of the morphological and geographical differences in Perilla grown and naturally occurring in South Korea, which will aid research on crop evolution and differentiation, as well as Perilla breeding programmes.