Amorphophallus variabilisBlume, a member of Araceae, is a native tuber crop in Java, Madura and Kangean Islands, Indonesia. The plant showed high variations in morphology. However, genetic variations at molecular level have not been well studied. Amplified fragment length polymorphism (AFLP) was carried out using 8 primers combination of EcoRI and MseI on 78 accessions collected from 28 sites in Java, Indonesia. Results showed that AFLP markers able to generate polymorphism among accessions. A total of 220 polymorphisms were found. The differences among accessions at the genetic level were high, and 5 clusters were constructed. Grouping was independent of geographical origin, similar to clustering of morphological characteristic of flowers as in the previous report. Accessions from one site composed of one to four different cluster groups, showed that variation in single site was observed. Regarding conservation program of the A. variabilisin natural population, it is reasonable to protect one bigger site rather than many small sites, but it should be recommended to maintain conservation areas in several districts. Further study on population structure should be carried out to explain such variability. Keywords: genetic diversity, iles-iles, molecular marker, morphology, tuber crop - Santosa, Edi; Department of Agronomy and Horticulture, Faculty of Agriculture, Bogor Agricultural University