Several herbicidal chemicals are available for use in agriculture to increase the yield. Despite their usage commonly, they have impacts on crops. Related with this, in the current study, the effects of a widely used herbicide Roundup, which has glyphosate as the active ingredient. Molecular and spectroscopic approaches were combined together in order to investigate the effects of glyphosate on Zea mays. Depending on the EC50 value that reduce the root growth to 50%, three different concentrations of Roundup were used as 4 ml/L, 8 ml/L and 16 ml/L. They were applied to Z mays seeds for 48 and 72 hours. For RAPD (Random Amplified Polymorphic DNA) PCR analysis; 8 of 10 RAPD primers produced band patterns and it was found that five RAPD primers among them produced polymorphic band patterns and then were used to produce a total of 61 bands. Value of polymorphisms was 32.78%. Genomic template stability changed in RAPD profiles at various Roundup concentrations. In addition to PCR analysis, the root samples were studied by Fourier transform infrared (FT-IR) spectroscopy in order to obtain the effects of Roundup on the quantity of biomolecules, membrane fluidity, cell wall components, lipid and protein structure of Z. mays. Each concentration of Roundup caused significant effects on Z mays cells, particularly, the most effective concentration level was found to be 16 ml/L. Our corresponding results revealed that Roundup has prominent impacts on structure and function of biomolecules of Z. mays, all of which might be important for its growth. In conclusion, the combination of RAPD and spectroscopic analysis would offer efficient tool to determine the effects of any pesticides on plant cells.