The rhizome of Belamcanda chinensis (belamcanda sinensis/Shegan) is an important traditional Chinese medicine, which is often used to treat lung diseases. However, soft rot disease seriously threatens the production of B. chinensis, causing its rhizomes to rot and the entire plant to die. Based on morphological characteristic and multigenic phylogenetic analyses of 16S rDNA, pel (pectate lyases encoding genes) and mdh (malic dehydrogenase encoding genes), the pathogenic isolates were identified as Dickeya fangzhongdai. One representative isolate SG-17 was selected for biological characteristics and pathogenicity tests analysis. The results showed that the optimum temperature and pH for SG-17 growth were 28 °C and pH 6, respectively. SG-17 caused typical soft rot symptoms on healthy B. chinensis plants, and produced symptoms of similar severity on Iris japonica (fringed iris) and Iris tectorum (iris), the other two species in Iridaceae family of economic and ornamental importance. Moreover, we also evaluated the impact of SG-17 on the contents of bioactive ingredients in B. chinensis rhizomes. The results show that the contents of tectorigenin and irigenin of B. chinensis rhizomes were increased significantly after infected with SG-17, while the contents of irisflorentin was decreased. As revealed by bactericides screen experiments, Ethylicin and Carbendazim · tetramethylthiuram disulfide exhibited good antibacterial activities, which could be used as the preferred agents for the control of soft rot of B. chinensis. As far as we know, this is the first report of Dickeya fangzhongdai causing soft rot on B. chinensis in the world.