Genetic diversity within the azuki Vigna angularis (Willd.) Ohwi and Ohashi genepool has not been extensively examined with molecular markers. The objectives of this study were to: (i) use RAPD and AFLP analyses to assess the genetic similarity among selected azuki accessions from distinct production regions in Asia, and( ii) compare the utility of the two DNA marker systems for evaluating similarity. Results also will provide information for parental selection in a breeding program. Fifty‐seven RAPD and 214 AFLP bands were used to assess genetic diversity among 58 azukia acessions. Thirty percent of the RAPD and 18% of the AFLP amplification products were polymorphic among accessions. One AFLP primer pair detected a mean of 11.3 polymorphic bands per reaction versus a mean of 3.2 for each RAPD primer. On the basis of Jaccard's similarity coefficients (JSCs), higher level of molecular genetic variation was detected among accessions evaluated in this study than in other diversity assessments of azuki. Mean JSC based on AFLP data was significantly higher than that obtained from RAPD data (0.71 and 0.52, respectively), and results from phylogenetic analyses varied between DNA marker systems. A substantial difference in the number of polymorphic bands detected through AFLP versus RAPD analysis may have influenced these results since the ability to resolve genetic relationships among genotypes is related to the number of polymorphisms detected. Cluster analysis revealed groupings among accessions; however, no apparent correlations with putative geographic origin were detected. Results of this study suggest that the level of genetic diversity among selected azuki accessions should be sufficient for developing an intraspecific mapping population.