The present study evaluated genetic variability of superior bael genotypes collected from different parts of Andaman Islands, India using fruit characters and random amplified polymorphic DNA (RAPD) markers. Genomic DNA extracted from leaf material using cetyl trimethyl ammonium bromide (CTAB) method was subjected to polymerase chain reaction (PCR) with 12 polymorphic primers. A total of 476 polymorphic loci were identified with mean value of 39.66 bands per primer and 63.99% polymorphism. Application of unweighted pair group method using arithmetic average cluster analysis generated three genotypic groups. 'Bael-5' and 'Bael-8' were most similar genotypes whereas 'Bael-7' and 'Bael-1' were extreme divergent. The clusters based on molecular data were not in agreement with the morphological traits in most of the cases as low level of correlation was observed between the classification methods based on fruit characteristics and RAPD markers. The bael genotypes were found to have considerable genetic variability, demonstrating the importance of RAPD markers to analyse each genotype in a collection in order to efficiently maintain the germplasm collection for genetic improvement of bael.