Amplified fragment length polymorphism (AFLP) analysis was conducted to investigate the level of polymorphism in four jute genotypes including two genotypes (JRC 321 and CMU 010) of Corchorus capsularis (the white jute) and two genotypes (JRO 524 and PPO4) of Corchorus olitorius (the tossa jute). Out of 1024 primer combinations that were tried, as many as 281 combinations of selective primers (13 EcoRI and 64 MseI) were selected, which produced a total of 9092 amplicons, including 752 (8.3%) polymorphic bands in C. capsularis and a total of 8856 amplicons including 1477 (16.7%) polymorphic bands in C. olitorius. The average number of bands/primer combination was 32.3 for C. capsularis and 31.5 for C. olitorius. For C. capsularis, highest polymorphism of 56.6% was shown by primer combination E35M50, while for C. olitorius highest polymorphism of 50% was shown by E41M91. In C. olitorius, 30-50% polymorphism was observed with 27 primer combinations, but in C. capsularis only 3 primer combinations gave this level of polymorphism. Similarly, in C. capsularis <10% polymorphism was detected by 115 primer combinations while in C. olitorius, <10% polymorphism was shown by only 56 primer combinations. These results indicate a higher level of polymorphism in C. olitorius relative to that in C. capsularis. The occurrence of such a large number of polymorphic AFLP markers will facilitate preparation of molecular maps and QTL analysis in jute.