In this study, 18 simple sequence repeat (SSR) primer sets were used to analyze the genetic diversity, genetic relationships, and population structure among 96 accessions of the two cultivated types of Perilla crop and their weedy types in East and Southeast Asia. A total of 168 alleles were identified at all the loci with an average of 9.3 and a range between 3 and 18 alleles per locus. Of the 168 alleles, 21 alleles (12.5%) were private, 67 alleles (39.9%) were rare (frequency < 0.05), 96 alleles (57.1%) were detected at an intermediate frequency (range, 0.05 - 0.50), and five alleles (3.0%) were abundant (frequency > 0.50), respectively. The gene diversity values varied from 0.443 to 0.898 with an average of 0.749. The PIC values varied from 0.397 to 0.890 with an average of 0.721. The gene diversity of each locus for accessions of cultivated var. frutescens, weedy var. frutescens, cultivated var. crispa, and weedy var. crispa were respectively showed 0.662, 0.744, 0.540, and 0.584. On the analysis of population structure using software program STRUCTURE 2.2, the 96 Perilla accessions were divided into Groups I, II, and admixed group. The phylogenetic tree revealed that the 96 accessions cluster into three major groups. No clear geographic structure and also between two cultivated types of Perilla crop and their weedy types were detected. The present study has demonstrated the utility of SSR analysis for the study of genetic diversity, genetic relationships and population structure among 96 accessions of the two cultivated types of Perilla crop and their weedy types in East and Southeast Asia. In our study, SSR markers helped improve our understanding of the genetic diversity, genetic relationships, and population structure of the two cultivated types of P. frutescens and their weedy types in East and Southeast Asia.