Abstract: The genetic diversity of 28 vegetable daylily germplasms in China were studied based on 19 morphological characteristics as well as the start codon targeted polymorphism(SCoT) markers of the plants. The agronomic analysis showed that the variations on 10 quantitative indices among the germplasms were large with the variation coefficients ranging from 14.5% to 37.2%. The highest coefficient was found on tiller number, followed by leaf width at 35.5%, while leaf length being the lowest. The results obtained from the molecular marker clustering were similar, and both methods classified the germplasms into two classes.However, the SCoT technique clustered the 3 newly introduced germplasms into Class Ⅰ (red flower) and could satisfactorily distinguish Wu Yue Hua from Liu Yue Hua while the morphological approach failed to do so. It appeared that the utilization of SCoT markers was faster, more sensitive and accurate than that of the agronomic properties for the identification of the daylily cultivars among various germplasms.