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Background: Phaseolus lunatus L. is a type of legume which is potential to become food source for Indonesians as it is rich in nutrition. Unfortunately, its potential as food source rich in nutrition is under-appreciated by most Indonesians. In addition to the decreasing number of P. lunatus L. population, researches which concern on the diversity and diversification of beans in Indonesia are limited in all sorts. Species diversity study is an interesting yet important field of research. However, diversity and the relation among Phaseolus species in Indonesia are hardly be found. Aims: This study aimed at investigating the diversity of P. lunatus L. in East Java, Indonesia based on RAPD marker. Materials and Methods: In this study, P. lunatus L. collected from some areas around East Java, namely Tulungagung, Kediri, Malang, Probolingo, and Madura. This study includes two main stages: (1) DNA isolation following the CTAB method Doyle and Doyle (1987) modified by Maftuchah and Zainudin (2010); and (2) Electrophoresis of the isolated results using RAPD OPA6 (GGTCCCTGAC) primers, OPA8 (GTGACGTAGG), OPA10 (GTGATCGCAG), OPA20 (GTTGCGATCC), OPC19 (GTTGCCAGCC), OPD8 (GTGTGCCCCCC), OPA10 (GTGATCGCAG), OPA20 (GTTGCGATCC), OPC19 (GTTGCCAGCC), OPD8 (GTGTGCCCCCC) OPE15 (ACGCACAACC), OPE16 (GGTGACTGTG) developed by Operon technologies, Alameda, California. Data analysis was performed by looking at the banding pattern that appeared from the electrophoresis results at each primary locus. After that the DNA band pattern data was then converted to binary data. Furthermore, from the bands that appear will be seen the percentage of polymorphic and monomorphic bands. Then, the phylogenetic tree was compiled using PopGen software. Results: Variation of genotypic diversity in 15 genotypes resulted in 68 RAPD bands being scanned from 10 primary oligonucleotides (OPA6; OPA8; OPA10; OPA20; OPC19; OPD8; OPD12; OPE8; OPE15; OPE16) with an average of 6.8 bands per primary. Of the 10 primers used to produce 68 bands, with varying sizes of DNA fragments. The results of the amplification seen almost all polymorphic DNA bands. The total bands produced from 10 primers were 68 DNA bands. Primers that produce the smallest number of bands were OPA10 and OPA20 primers, while primers that produce the most bands were OPD12, producing 9 bands. There were 9 primers which have 100% polymorphism. Cluster analysis of 68 pattern bands produces a phylogenetic tree using Neighbor-Joining method, with similarity coefficients ranging from 64% -100%. In the genetic similarity coefficient, P. lunatus formed two groups, namely the main cluster (cluster A) consisting of genotypes 7, 8, 13, as well as 14 and the second main cluster group (cluster B) consisting of genotypes 2, 4, 16, 18, Prb1, Prb2, Prb3, Prb4, as well as Prb 5. Conclusion: PCR-RAPD results using 10 random primers informed that genetic variation among 15 P. lunatus L. genotypes was found in the range of 0-36%.