Department of Microbial Chemistry was born out of Chemical Extraction Group in the Department of Antibiotics, Chinese Academy of Medical Science in 1956. In 1958, the Institute of Antibiotics was established on the basis of the Department of Antibiotics, accordingly, the group was expended as Department of Chemical Extraction. In these periods, the group leaders or dean were always Da-bin Huang and Wen-xiang Wang. From 1980 to 1985, the dean were Wen-xiang Wang, Chang-qin Qi and Wen-zao Jin. After 1985, the department was divided into three including Department I of New Antibiotics headed by Jian-bo Wu and Tian-jue Yao; Department II of New Antibiotics headed by Wen-zao Jin and Yu-qin Zhang; Department III of New Antibiotics headed by Qi-wei Yu and Hong-zhang Xu. After the Institute of Antibiotics changed name as Institute of Medicinal Biotechnology in 1987, Department I and II of New Antibiotics were merged into Department of New Antibiotics headed by Jian-bo Wu, Wen-zao Jin and Tian-jue Yao in the end of 1980s, meanwhile, Department of Antibiotic Development headed by Hong-zhang Xu was established on the basis of Department III of New Antibiotics. In 1993, the two departments were combined as Department of New Antibiotics, which were headed by Jian-bo Wu, Wen-zao Jin and Hong-zhang Xu from 1993 to 1997 and by Jian-bo Wu, Hong-zhang Xu and Cheng-hang Sun from 1997 to 1999. In 1999, The Department of New Antibiotics finally was replaced as Department of Microbial Chemistry headed by Jian-bo Wu, Hong-zhang Xu and Cheng-hang Sun. The head of the department were Jian-bo Wu and Ru-xian Chen from 2005 to 2007, and Ru-xian Chen and Cheng-hang Sun from 2008-2016. From 2016 till 2021, the Dean of Department of Microbial Chemistry is Cheng-hang Sun.

The Department of Microbial Chemistry has always been playing an important role during the past several decades, since the research works carried out in the department are essential in providing new secondary metabolites as leading compounds and an important link in the systematic engineering for antibiotic R&D. Hundreds of antibiotics including important clinic antibiotics were isolated, purified and structurally elucidated including clinic important antibiotics including penicillin, erythromycin, terramycin, kanamycin, zhengdingmeisu, griseoflavin, spectinomycin, colistin, vancomycin, trichomycin, paromomycin, mithramycin, zhengguangmeisu, chuangxinmycin, bleomycin, daunorubicin, pingyangmycin, ribostamycin, midecamycin, acetylspiramycin, sirolimus, teicoplanin, boanmycin, zhongshengmycin, agricultural anti-120 etc. The Department of Microbial Chemistry has undertaken multiple national research projects, such as the National Natural Science Foundation of China, National Programs for Science and Technology Development, National High-tech R&D Programs of China (863 Program). During the period of the 11st, 12ed and 13th "Five-Year Plan”, the department undertook many important tasks in national mega-projects for innovative drugs and the CAMS Innovation Fund for Medical Sciences. Since 1984, more than 100 Master and Ph.D students have graduated from this department. Over 200 scientific papers or monographs and 24 authorized patents have been published or contributed by researchers in the department. Additionally, 8 national prizes and 19 ministerial or provincial prizes were awarded for their scientific achievements. In recent decades, supported by the central government, the teaching facilities and equipment of the laboratory in the department have been completely updated and upgraded.

The main task in the department is still the discovery of leading compounds from microorganisms, for which, the research was divided into several branch including: 1) bioprospecting on pharmaceutical microorganisms from special environments or niches such as Desert, salt lake, Karst Caves and Mangrove, Marine etc., 2）Discovery of new compounds and its producing strains by bioassay, chemical screening, genomic mining, molecular networking, metabolomics etc., 3) isolation, structural elucidation and modification or total synthesis of compounds from microorganisms.

Research groups:  SUN Chenghang's group,  XIE Yunying's group .