The aim of present research was to study genetic diversity among twelve different accessions of Momordica charantia L., growing in eight different districts of West Bengal using morphological characters, RAPD and SCAR markers. Five plants for each of 12 accessions was selected and were examined for 13 morphological characters. RAPD analysis of 12 accessions of M. charantia was performed with 17 decamer primers from a total of 23 primers. A dendrogram was constructed by cluster analysis to establish the affinity and relationship between the 12 accessions of Momordica charantia, using average linkage between the groups. Accession specific Sequence Characterized Amplified Region (SCAR) marker was developed from accession 12 sequences, using primers designed from both the flanking ends of RAPD primer. When morphological characters were considered the 12 accessions of M. charantia could be clustered into 2 groups. Group I comprised of the accessions belonging to variety muricata and Group II comprised of the accessions belonging to variety charantia. When RAPD markers were considered, dendrogram constructed by cluster analysis with average linkage between groups produced two major clusters - Cluster I comprised of the accessions belonging to variety muricata. Cluster II comprised of the accessions belonging to variety charantia and variety muricata. Thus the clustering pattern based on RAPD markers was not in accordance with the grouping based on morphological characters. Development of accession specific SCAR marker (855 bp) in accession VI2 was used to distinguish it from different accessions of M. charantia their by validating the RAPD marker. Molecular markers (RAPD, SCAR) were found to be more effective as compared to morphological marker in assessing the genetic diversity of twelve different accessions of M. charantia. © 2010 Asian Network for Scientific Information.