The essential oil (EO) of Cistus ladaniferus was separated into non polar, moderately polar and polar fractions by column chromatography. The EO and its fractions were analysed by gas chromatography in combination with retention indices [GC-(RI)] and 13C nuclear magnetic resonance (13C NMR) spectroscopy. A minimum inhibitory concentration (MIC) assay was used to evaluate their antibacterial activity against Gram-positive and Gram-negative pathogens of clinical relevance, including a multi-drug resistant (MDR) strain. The most polar fraction, constituted by mono- and sesquiterpene alcohols, strongly inhibited the growth of all tested bacteria with MIC values ranging from 0.05 to 0.8 mg/mL. More importantly, this fraction displayed high activity against the MDR strain of Enterobacter aerogenes EA289. Transmission electron microscopy (TEM) observations of the MDR bacteria treated with the terpene alcohol-rich fraction revealed cell wall distortion with an outer cytoplasmic membrane detachment. The susceptibility of the MDR strain of E. aerogenes EA289 to the polar fraction of C. ladaniferus oil suggests the possible use of these natural products to treat infections caused by highly resistant bacteria.