The major difference is that RFLP is the simplest technique among the three. RFLP requires previous knowledge of target DNA whereas RAPD and AFLP don’t. AFLP employs the use of specially synthesized adapter molecules, and RAPD requires the use of arbitrary oligonucleotide primers of known sequences but RFLP doesn’t employ such complex molecules. RFLP is more commonly used in commercial practice than the other two techniques.