Abstract. Mas’udah S, Fauziah, Hapsari L. 2019. Cluster analysis of Dioscorea alata accessions of Purwodadi Botanic Gardens (Indonesia) collection based on morphological characteristic and SSR markers. Cell Biol Dev 3: 6-12. Morphological characteristics of D. alata accessions show a high diversity, especially the tubers which have varying form, size, weight, color, and flesh. Classification and naming of D. alata accessions generally using different local names in each region in which causing problems. This study aimed to classify 20 accession numbers of D. alata collection of Purwodadi Botanic Garden collected from East Java based on tuber morphological characteristics and simple sequence repeat (SSR) molecular markers. Based on the morphological characteristic, the accessions showed high variation. From seventeen characters observed, two characters were similar and 15 others were diverse. The main morphological characters that contribute to the cluster were tuber skin color, tuber shape and the color of the inner skin of the tuber. Clustering result based on DNA amplification showed different group compared to the morphological characters cluster although some accessions with close morphological characters were in the same molecular group. The accession origin could not be used as the group marker. Marker E11 and A7 have the highest polymorphisms in this experiment. As conservation strategies, accessions with high-level similarity could be represented by one accession for maintenance efficiency. Conserving species until varieties level that has different characters could be enriched germplasm for breeding development.