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Retama raetam (RR) and R. sphaerocarpa (RS) are shrubs growing in Algeria desert areas, where are commonly used as healing remedies because of their antiseptic, antipyretic and anti-diarrheal properties. Phytochemical studies have shown that these species are very rich in flavonoids (isoflavones) and alkaloids (quinolizidine and bipiperidyl). The aim of this study was to compare the chemical composition of both Retama species by GC/MS and LC/MS and to determinate their antimicrobial activity of two Retama species growing naturally in Algeria. Ten alkaloids and seven flavonoids were identified in cladodes of RR and RS. The quantitative analysis showed that the most abundant flavonoid of both the aqueous extract from RR and RS was the isoflavone genistein (610.0 +/- 2.8 and 408.0 +/- 14.1 mg/100 g respectively), whereas sparteine was the predominant alkaloid in RR and retamine in RS. The antibacterial activity of Retama extracts against standard strains was performed by minimum inhibitory concentration (MIC), and by the disc diffusion method (expressed by inhibition zone, IZ). Both Retama species showed the best activity against Staphylococcus aureus and methicillin-resistant S. aureus (MRSA), being RS aqueous extract more active than RR aqueous extract, with MIC 125 mu g/mL and bactericidal activity against both strains.