Characterization of germplasm resources of confectionary sunflower is critical to assess collection diversity. Seventy germplasm representing 12 provinces of China was characterized using eight amplified fragment length polymorphic (AFLP) primers and 17 morphological descriptors. Euclidean distance were used for AFLP and morphological data ranged from 0.32 to 1.56 and from 0.30 to 1.48, respectively. No two germplasm had a distance of zero, showing there were no duplicate entries. Cluster analysis of the AFLP data determined by SAS showed that 70.0% of the total germplasm (49 entries) were included in two main clusters I and II. A wild germplasm was single in the end cluster which is at 1.56 distance level to other clusters. For morphological data, 75.7% of the germplasm (53 entries) were in two main clusters II and III. This clustering pattern for AFLP and morphological data suggested that unique germplasm were generally underrepresented in the collection. The morphological-based clusters showed some locality separation by germplasm origin, but in general, the origin did not correspond closely with the clustering pattern. Principal component analysis (PCA) showed that the first seven principal components accounted for 81.33% of the total variation, of which 43.05% was contributed by the first two principal components.