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The purpose of this study was to identify the chemical components in root extracts of Saponaria cypria, an endemic species of Cyprus. Subsequently, the synergistic bioactivity of its root extracts through different extraction procedures was also investigated for the first time. A total of nine saponins, along with six phenolic compounds, were identified and quantified using the UHPLC/Q-TOF-MS method. Additionally, S. cypria root extracts demonstrated antibacterial potential against Escherichia coli, Staphylococcus aureus, Enterococcus faecalis and Salmonella enteritidis. S. aureus presented the highest susceptibility among all bacteria tested. These findings provide the first phytochemical data regarding the saponin, phenolic content and antimicrobial activity of S. cypria extracts, indicating that the Cyprus saponaria species is a rich natural source for bioactive compounds with a potentially wider bioactivity spectrum.