This study was to elucidate the intra-species variation of wild yam in Taiwan. A clusters analysis based on 30 morphological characteristics grouped the 39 accessions into 3 main clusters. The results also indicated that significant difference of morphological characteristics of wild yam D. pseudojaponica were detected between Ilan population and Taipei population. Genetic variation were detected among the clones of D. pseudojaponica in local population and the clones of D. doryphora in Hengchuen peninsula.