Chromoblastomycosis is a chronic, cutaneous and subcutaneous infection caused by members of the order Chaetothyriales and commonly found in China. Among the etiologic agents, members of the genus Cladophialophora are predominant in northern China. Alternatively, Fonsecaea spp. are particularly common in southern China. However, the identification of Fonsecaea isolates recovered in China is difficult due to the fact that different species lack distinctive morphological characters. Therefore, the identification of 24 Fonsecaea isolates from symptomatic patients were re-evaluated by using morphology, ITS rDNA sequence diversity and partly through the use of randomly amplified polymorphic DNA (RAPD) typing. Twenty strains, including a morphological mutant were found to be Fonsecaea monophora, while four strains corresponded to F. pedrosoi. We have demonstrated that Fonsecaea monophora is the predominant etiologic agent of chromoblastomycosis in southern China and populations showed marked geographic structuring.