Black potato (Coleus tuberosus Benth.) is one of functional food. Propagation of this plant is easy to conduct and grow at various altitudes. Black potatoes are possible to widely distributed in various regions in Yogyakarta. This study aimed to examine the diversity and phenetic relationship of black potato samples based on morphological and leaf anatomical characters in Special Region of Yogyakarta as the first step in plant breeding. Samples were collected by survey method and interviewing. Samples were collected in Yogyakarta composed of tubers, stems, leaves, and flowers. Samples were characterized based on morphological and leaf anatomical characters, followed by scoring, standardization, and calculating the SI (Similarity Index) between samples (OTUs). Clustering analysis was done using UPGMA (Unweighted Pair Group Method with Arithmetic Averages) to create dendrogram of phenetic relationship. Deciding how many clusters formed in dendrogram supported by phenon line 0.7 and dominant characters supported by PCA (Principal Component Analysis). Results showed that the variation of black potatoes morphologically on stem, leaves, and tubers. Anatomically, variations were found in stomata, epidermis, xylem, and palisade parenchyma. Dendrogram based on morphological character divided into four clusters. Dominant character formed A cluster was leaf position anomaly, B cluster was adaxial leaf color, C cluster was stem erect, and D cluster was leaf rigid. Dendrogram based on leaf anatomical character divided into three clusters. A cluster formed because the similarity of palisade parenchyma layer, B cluster was neighbor cell of stomata margin shape, and C cluster was xylem arrangement.
