Nigella sativa L. and Matricaria chamomilla L. are used widely as traditional medicine since ancient ages because they contain some substances believed to have antitumor, anti-oxidants, anti-inflammatory, and antimicrobial activities. Objective: to assess the quantitative assay for alkaloids, tannins, phenolic acids, saponins and flavonoids in Nigella sativa L. and Matricaria chamomilla L. extracts with evaluation of their antimicrobial activity. Results: the quantitative assay for Nigella sativa L. and Matricaria chamomilla L. extracts were total flavonoids (295.21±0.51 and 263.12±1.05 rutin Eq/g DW), total phenolic acids (388.60±1.02 and 302.10±0.88 μg gallic acid equivalent (GAE)/mg DW), total tannins (1.23±0.11 and 1.33±0.13%), total saponins (1.71±0.10 and 1.66±0.16%)and total alkaloids (2.01±0.20 and 1.07±0.14 %), respectively. Based on the observed results, Nigella sativa L. and Matricaria chamomilla L. extracts contain active anti-microbial substances. Diameters of the inhibition zones of Nigella sativa L. and Matricaria chamomilla L. extracts were about (17 and 15 – 14 and 18 – 8 and 8 – 12 and 10 – 15 and 13 – 16 and 14 mm) against Staphylococcus aureus, Staphylococcus haemolyticus, Escherichia coli, Klebsiella pneumoniae, Candida albicans and Candida glabratarespectively. The minimum inhibitory concentrations MICs of Nigella sativa L. against the bacterial and candida strains ranged from 250 μg/ml to 500 μg/ml and MLCs ranged from 500 μg/ml to 1000 μg/ml. where the MICs values of Matricaria chamomilla L. against the bacterial and candida strains ranged from 500 μg/ml to 1000 μg/ml and minimum lethal concentrations MLCs ranged from 1000 μg/ml to 2000 μg/ml. Conclusion: this study demonstrates the Nigella sativa L. Matricaria chamomilla L. efficacy as an therapeutic agents in the treatment of many microbial diseases to provide a comprehensive guide for pathologists