Black mustard (Brassica nigra L.) contains defensive chemical compounds that hampered the growth and the development of several plants including barley. Therefore, the present study was conducted during 2015–16 at Al-Balqa Applied University of Jordan. different genotypes of barley in Jordan were studied for the allelopathic effect of mustard. The results revealed that the relative water content of shoot was not affected by the studied extract. Contrarily, root relative water content of barley was significantly influenced by the allelopathic mixture of leaf and whole plant. The differential response of root and shoot of barley to the allelopathy of Brassica seems to be related to the fact that extract from Brassica primary influenced membranes permeability. Moreover, result found that the expressions levels of Superoxide Dismutase (SOD) genes varied but not varied according to genotypic of the studied barley. Ct values (a measure of relative gene expression) revealed that the Mn-SOD gene was the most expressed among the studied genotypes. The higher transcript (mRNA) of this gene at leaf extract was found to be at concentration of 4 g/100 mL and it was upregulated about (12 folds) in Irbid genotype. On the other hand, at 12 g/100 mL the gene was also highly expressed (15 folds) in Athroh genotype. Moreover, at 20 g/100 mL the gene level was highly upregulated (32.65 folds) in Irbid genotype. Whereas, in the genotype of Mutah and Acsad, the gene expression was downregulated when barley was subjected to 4 g/100 mL of leaf material and varied about 0.81-fold and 0.78-fold. On the other hand, the Mn-SOD gene under plant materials at 4 g/100 mL were found to be upregulated in the Amman genotype. Whereas at 12 g/100 mL Mn-SOD was found significantly higher (about 24-fold) in Acsad and less regulated about (0.084) in Maan genotype. The results presented in this work suggest that allelopathic effects of Brassica nigra is genotypic and concentration dependent.