As one of important wild germplasm resource in “Saccharum complex”, Erianthus arundianceus is widely distributed in China, but has being used inefficiently in sugarcane genetic breeding research. In this study, we gathered 147 clones of Erianthus arundianceus from 9 provinces in China and planted in National Nursery of Sugarcane Germplasm Resources as original materials. Firstly, 58 clones were selected based on phenotypic data to construct primary core collection and then 16 clones were selected based on SSR and AFLP molecular markers to construct mini core collection, which occupied 39.46% and 10.88% of original materials respectively. Through comparative analysis of phenotypic and molecular genetic diversity parameter, the core collection of E. arundianceus was proved to be a good representative sample. Finally, we discussed how to build and use focus on core collection of E.arundianceus effectively in sugarcane germplasm resources and genetic breeding research. This paper aims to provide reference for construction and application of core collection from wild populations of “Saccharum complex”, and to promote transformation of future research focus from quantitative conservation to innovative utilization.