Abstract: In this study, we investigated the leaf anatomical structure, pigment content, and photosynthetic characteristics of Perilla frutescens from 9 sites. The results showed that all the leaves of P. frutescens from the 9 sites were bifacial leaf, containing a palisade tissue with onelayer tightly arranged long columnar cells and a spongy tissue with 2 or 3 layers cell. Furthermore, there were more stomata (mostly oval) and glandular hairs in the lower epidermis of the leaves. The diameter and density of stomata of P. frutescens significantly differed among different sites. The P. frutescens from Yantai had the largest stomata diameter, and that from Wuxi had the greatest stomata density. Nevertheless, the stomatal diameter and density of the P. frutescens from Nanjing were the minimum. The contents of chlorophyll and anthocyanin of P. frutescens from the different sites showed significant differences. The more purple leaf color was, the higher anthocyanin content and the lower chlorophyll content were. However, the leaf of the P. frutescens from Baoding, Handan and Xingtai had higher contents of chlorophyll and anthocyanins. There was a negative correlation between the anthocyanin content and net photosynthetic rate in P. frutescens leaves. For example, the P. frutescens from Yantai had a lower anthocyanin content but higher net photosynthetic rate, while the P. frutescens from Nanjing had a higher anthocyanin content but lower net photosynthetic rate. The leaf anatomical structure and pigment content of P. frutescens were significantly different among different sites, and they had a certain correlation with net photosynthetic rate. This study laid a foundation for further study on germplasm resources and breeding of P. frutescens.