In order to develop SSR markers suitable for Perilla frutescens and study the genetic diversity and population division of P. frutescens, in this study, 66 pairs of SSR primers from Perilla and its relatives were used to amplify 42 Perilla materials from different sources. The results showed that: 15 pairs of primers were polymorphic in 42 materials, 54 bands were obtained by amplification, with an average of 3.6 bands per pair of primers, and 51 bands were polymorphic, accounting for 94.4% of the total amplification bands. The UPGMA method was used to cluster analysis. At SM=0.67, the P. frutescens was divided into two main clustering groups.GroupⅠ was P. frutescens var. frutescents, GroupⅡ was P. frutescens var. crispa and GroupⅠ could be further divided into five subgroups. The phenotypes of each subgroup had a certain characteristic difference. The results of this study could provide reference for the research of the Perilla genetic relationship and resources identification.