RAPDs have several advantages over RFLPs and can be used as their substitute in several studies. The main advantages include the following:
(i) Since same primers with arbitrary sequences can be used for different species, no species specific probes are needed for different species as required in RFLPs. For instance, primers that provide polymorphic markers in maize, also provided polymorphic markers in soybean, Arabidopsis, humans, Neurospora, etc.
(ii) Collection of data using RAPDs proceeds much more quickly than, those using RFLPs, since there are fewer steps involved. It has been shown that generation of RAPD data is five times quicker than RFLPs. Important properties of RFLPs and RAPDs II are presented in for comparison.
RAPD techniques may also be combined with RFLPs to increase the efficiency of molecular markers for genetic analysis. A RAPD marker, known to be polymorphic, may be labeled and used as a probe for RFLP, analysis, thus eliminating the need for recombinant DNA cloning of probe in bacteria.