The aim of this study was to evaluate the toxicity of black cumin (Nigella sativa) extract on germination and growth of flixweed (Descurainia Sophia) seedlings grown in wheat (Triticum aestivum) fields, isolation and identification of important bioactive compounds of its aqueous extract. Two factorial experiments were conducted in a completely randomized design with three replications. In each experiment, the treatments included two levels of black cumin aqueous extract (root and shoot) and four concentrations of the extract (0, 50, 100 and 150 mL/L). The results showed that the highest plumule length belonged to wheat treated with 50 mL/L of black cumin root extract and the lowest to flixweed treated with 150 mL/L of black cumin shoot extract. With increasing the concentration of black cumin extract, the amount of seedling vigor index decreased significantly. In addition, the inhibitory effect of black cumin shoot extract on seedling dry weight and germination percentage was higher than the root extract. In root and shoot extract of black cumin, flavonoid compounds (12.9% and 16.7%, respectively), phenol (19.4% and 26.7%, respectively), terpenoids (14.5% and 19.2%, respectively) were observed. Inhibition of germination and seedling growth of flixweed was attributed to important inhibitory compounds including polyphenols, flavonoids such as tricarboxylic acids, alkaloid compounds such as magnetofluorine, myristicin, norargemonin and niglamine. In general, it is concluded that black cumin extract with strong toxicity to weeds can help the development of biocides.