Abstract: Qingliu County in Fujian is one of the most important gerbera producing areas in China. Recently, the root rot disease is becoming epidemic and serious in the county. The present study sampled and isolated pathogenic fungi from the plant roots that were infected by the disease. The morphology and molecular identification analyses on the samples indicated that the pathogens, Phytophthora cryptogea, Fusarium oxysporum, Colletotrichum gloeosporioides and F. solani were likely the culprits, with P. cryptogea and F. oxysporum being most numerous. After a Koch's theorem verification, P. cryptogea was further identified as the fungus that caused the root rot disease on gerbera in Qingliu County. The information is to be used for selecting control method and in further studies on the pathogen as well as its antagonistic microorganisms for bio-control on the disease.