Objective: Increasing use of medicinal plants in the treatment of infectious diseases are due to the development of multi-antibiotics resistant microorganisms, and had alerted our interest in the examination of some natural products. This study was carried out to investigate the antimicrobial activity of Jordanian propolis, black seed oil (Nigella sativa) extract, alone or in combination against clinically isolated microorganisms (bacteria and fungi).Methods: Jordanian propolis samples were collected. Aqueous and alcoholic extractions were done; black seed oil was extracted from Nigella sativa seeds. Seven clinical isolated microorganisms namely: Micrococcus luteus, Bacillus pumilus, Bordetella bronchisptica, Enterococcus fecalis, Bacillus subtilis, and Staphylococcus aureus, and one yeast strain namely Candida albicans were used. The antimicrobial activity was investigated by agar diffusion technique and microplate dilution to determine the MIC.Results: The results indicated that the alcoholic propolis extract showed higher antimicrobial activity than the aqueous propolis extract. The antimicrobial activity of black seed oil was significantly higher than that of the propolis. Mixing propolis with black seed oil showed synergism effects against some microorganisms as Enterococcus fecalis (24±1.1), Bordetella bronchisptica (20±0.9) and Candida albicans (40±2.3), and additive with others as Bacillus subtilis (28±1.8).Conclusion: Black seed oil and propolis might be used as a potential source of safe and effective natural antimicrobial in pharmaceutical and food industries