Two conodont zones were identified in the Yilan Formation of the Mode Section, Nandan County, Guangxi Province, the Polygnathus excavatus and P. nothoperbonus zones. In combination with previous research this suggests that a complete sequence of the lower Emsian polygnathid lineages cannot be recognized in any hitherto studied sections in South China because of the widespread clastic sediments of the lowermost Emsian. A comparison of the stratigraphic distribution of conodonts as well as the lithological transition among the Mode Section and previously studied sections indicates that the development of the carbonate sequence in South China during the Early Devonian transgression lies in a certain level of the P. excavatus Zone, showing an obvious chronological trend from south to north, and also that the differentiation of the platform and basinal facies of the Devonian in South China began in the lower P. nothoperbonus Zone.