Abstract: This paper deals with anatomical characteristics and microscopic constant numbers of 11 species and one variety of folk medicinal Swertia, which distribute in the regions from Hubei and Tibet of China to Toyama and Tokyo of Japan through Nepal.The waviness of the anticlinal walls and the ratio of the Feret′s diameter of the epidermal cells in the leaves are detected with the Image Analyze System (Olympus Optical Co. Ltd and Nippon Avionics, SP-500 SET) through the treatment of binarization.These taxa could be distinguished from each other by the characteristics such as types of vascular bundles, number of palisade cell layers, distribution of needle crystals and stomata, stomatal index, palisade ratio, ratio of Feret′s diameter and waviness of the anticlinal walls of the adaxial epidermal cells in leaves, etc.The results, especially application of Image Analyze System, provide a new method for identifying the botanical origin of crude leaf and herb drugs.