The average polymorphism information content (PIC) value for the SSR and AFLP marker systems was 0.41 and 0.47, respectively. Primer MJM136 for SSR and primer combination E-AGG/M-CTA for AFLP showed the highest PIC values (0.51 and 0.50, respectively), indicating they were the most informative primers for the assessment of genetic diversity in jute and that SSR and AFLP markers are useful for distinguishing jute genotypes.