The use of molecular markers to enhance plant breeding efforts is being widely studied. DNA-based fingerprinting technologies (RAPD and AFLP) have proven useful in genetic similarity studies. We estimated different maize (Zea mays L.) inbred lines and hybrids originated from mutant ones based on their genetic differences. We carried out RAPD analysis with different primers and the 707 (CCCAACACCC) and 792 (CAACCCACAC) primers with 50% similarities provided quite good DNA fragments. By applying the DNA based-AFLP technique, we had very dense DNA fingerprinting. We differentiated 15-32 polymorphic bands, the highest number of bands were found in P-T/H-CA (32). AFLP seems to be the more efficient method of comparing genetic similarities/differences among different genotypes.