This study was designed to compare the genetic effects of elevated carbon dioxide (CO2) and ozone (O3), alone or in combination, under irrigated and non-irrigated conditions on proteins and DNA of wheat (Triticum aestivum L.). Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), isozymes, random amplified polymorphic DNA (RAPD), and comet assays were used. SDS-PAGE analysis revealed distinctive polymorphisms (100%) based on the number of polypeptide bands (169) with molecular weights ranging from 300.0 to 24.00 kDa, band intensity, appearance, and loss of bands when compared with control samples. Six isozymes, malate dehydrogenase, amylase, leucine-aminopeptidase, esterase, peroxidase, and catalase, generated 100% polymorphism values based on zymogram number, relative front, and optical intensities. RAPD revealed 276 DNA bands with a distinctive polymorphism value of 92.31% based on the number of amplified DNA products, ranging from 45 to 1100 bp, and band intensity. In the comet assay, the highest extent of nuclear DNA damage was observed as tail length 8.70 μm, tailed DNA 8.01%, and tail moment unit 34.18 in non-irrigated O3-treated wheat nuclei. These results show that O3-treatment alone induced high levels of oxidative protein and DNA damage in wheat plant, especially in a non-irrigation system. Interestingly, CO2 in combination with O3 could ameliorate the negative impact of O3-oxidative stress. This study shows that protein and DNA biomarkers, and the comet assay, could be used for the reliable estimation of genotoxicity following the exposure of economic crop plants to air pollutants.