Herbicides are the most effective tool against weed flora in cereal crops that help to maintain and increase crop yields. This investigation was conducted in the winter season of 2018 to study the stress effect of three post-emergence herbicides including pinoxaden, tribenuron-methyl, and pyroxsulam on the biochemical changes at the molecular cell level of wheat. These herbicides were applied either lonely with a rate of 0.45 L.ha− 1, 22.5 gm.ha−1, and 0.16 Ib a.i/A, respectively, or in combinations together on three Egyptian varieties of bread wheat known as Misr1, Giza17 1, and Gemmiza 11. Firstly, the abovementioned herbicides were used at the recommended and half recommended doses with their combinations for these varieties to investigate DNA protein linkage as a signal effect of herbicides at the molecular cell level. Our data showed that the treatment of wheat varieties with the tested herbicides induced new bands with low and high molecular weights of 37.49, 40.08, 146.55, and 147.23 KDa with relative mobility of 0.1574, 0.1603, 0.2166, and 0.2168, respectively. These bands were not presented in the control treatment, suggesting that it might be used as a biochemical marker for plant defense genes. Meanwhile, the control treatment exhibited only five or six bands in the three varieties. However, the tested varieties showed that the same number of bands, the molecular weights of bands, and their relative mobility were significantly varied between the single and the combinations treatment of herbicides. The best treatment was achieved by the combination between pinoxaden and tribenuron-methyl at a recommended dose which induced a large number of protein bands compared to the control treatment on the wheat variety cv. Misr 1, which gave one band with low molecular weight 71.44 KDa at Rf 0.1854 and other with the highest molecular weight 147.23 KDa at Rf 0.2168, compared to the control treatment.