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Fenugreek ( Trigonella foenum-graecum ), an important spice crop belongs to the family Fabaceae. India is the largest producers as well as the largest exporter of fenugreek. Five common fenugreek varieties of India were included in this study for molecular analysis. For randomly amplified polymorphic DNA (RAPD) analysis, a total of 47 bands in the size range of 200 to 5000 bp were produced by examining across genotypes with 9 RAPD primers, with an average polymorphism of 62.4%. Total numbers of bands ranged from 3 (U407) to 7 (OPB-15). With 17 fluorescently labeled amplified fragment length polymorphism (AFLP) primer combinations (PCs), a total of 669 peaks in the size range of 50 to 538 bp were amplified. Total numbers of bands ranged from 21 (E-AAC/M-CT) to 60 (E-AAC/M-CAC). The mean genetic diversity (Nei's 1973) across all loci was found to be 23.83 and 2.1% with RAPD and AFLP markers, respectively. In all the fenugreek varieties, a total of 25 variety-specific AFLP markers were found. Phylogenetic trees among 5 plant varieties were constructed based on Nei's coefficient standard genetic distances using unweighted pair group method with arithmetic mean (UPGMA) method. For RAPD and AFLP analysis, Gujarat Methi-1 (GM-1) and Gujarat Methi-2 (GM-2) clustered together showed more similarities than other varieties. In fenugreek, RAPD markers were found more polymorphic than AFLP markers. RAPD markers also showed more diversity in comparison to AFLP markers, although the data generated for AFLP markers were more authenticated and reproducible than RAPD markers. Key words : AFLP, RAPD, genetic diversity, automated genetic analyzer, polymorphism.