Nicosulfuron (NS) is a chemical substance extensively used on maize (Zea mays L.) production as weed-killer (herbicide). It is very effective and destructive on weeds, but genotoxic effects of this herbicide on Z. mays has not been investigated. It is aimed with this study to investigate the genotoxic effects of NS herbicide on roots of germinated Z. mays grains. The NS was performed different doses (50, 125, 250, 500 and 750 ppm) during 24, 48 and 72 hours. DNA isolation from root samples was carried out using the CTAB method. DNA fragments from Z. mays genome were amplified by PCR technique using RAPD (Random Amplified Polymorphic DNA) and ISSR (Inter Simple Sequence Repeat) primers. In addition, root terminal cells of Z. mays were stained using 2% orcein and morphologies of cell nucleuses were investigated. Analyzed electrophoresis profiles of RAPD and ISSR-PCR have clearly indicated some changes such as the appearance of new bands or disappearance of bands as compared to the control. RAPD and ISSR-PCR analyses were clearly revealed that NS causes serious DNA sequence changes on Z. mays genome. Additively, some nuclear alterations were observed like micronuclei, irregular nucleus, nuclear buds, etc. depending on the increase of herbicide dose and exposure times.