The genus Ephedra belongs to ephedraceae family that contains about 67 species, most of which are being used in traditional medicines. In this research, two species were analyzed: stems and fruits of E. fragilis and stems of E. alata. Stems of both species were extracted with ethanol (95%, and 70%) and H2O, while fruits of E. fragilis were extracted with 70% ethanol. Results showed that 70% ethanol gave the highest percentage of stem extract (21.3%, and 17.7% for E. alata and E. fragilis, respectively), while fruits gave 35%. The 70% ethanol extract of E. alata gave the highest results for TPC, TFC and AA (42.53 mg Gallic acid/ g DE, 87.51 mg Rutin/ g DE, and 70.19 mg FeSO4/ g DE, respectively). On the other hand, 95% ethanol extract of E. fragilis showed the highest content of TPC, TFC and AA (32.81 mg Gallic acid/ g DE, 75.44 mg Rutin/ g DE, and 61.68 mg FeSO4/ g DE, respectively). Fruits of E. fragilis showed lower results for TPC, TFC and AA compared to stems of both species (14.47 mg Gallic acid/ g DE, 16.96 mg Rutin/ g DE, 38.57 mg FeSO4/ g DE). Stems of E. alata showed weak antimicrobial activity against both E. coli and S. aureus bacteria, but a strong activity against B. subtilis. Stems of E. fragilis were weak against E. coli and showed medium activity against S. aureus and B. subtilis, while fruits of E. fragilis had no activity against all bacterial species. Stem content of both ephedrine and pseudoephedrine were analyzed by a newly developed HPLC method revealing 0.0697% and 0.00411 for E. fragilis and 0.00453% and 0.175% for E. alata, respectively.