The aim of the present study was to characterize genetic diversity within a subset of 22 selected Lablabpurpureus accessions collected mainly from India using both morphological traits and amplified fragment length polymorphism (AFLP) markers. The high number of clusters formed from both morphological and AFLP analysis indicates considerable genetic diversity in the accessions used for the study. The clusters formed based on the AFLP data were not in agreement with the clusters formed based on morphological data found in the study, indicating the presence of discrepancy between the two methods. For selection of good parental material for heterosis breeding program, the diversity results obtained through AFLP can be used to correlate with the pedigree relationship and morphological traits for genetic improvement in dolichos crop.