Ionic liquids (ILs) have generated considerable attention recently because of their cytotoxicity and application as antibiotics. However, the mechanism of how they damage cell membranes is not currently well understood. In this paper, the antibacterial activities of two imidazolium-based ILs, namely 1-butyl- 3-methylimidazolium tetrafluroborate ([BMIM][BF4]) and 1-ethyl- 3-methylimidazolium tetrafluroborate ([EMIM][BF4]) have been investigated. The activity of [BMIM][BF4] on gram negative bacteria E. coli is observed to be stronger compared with the short chained [EMIM][BF4]. To explain this observation, the effects of these ILs on the self-assembled structures of model cellular membranes have been investigated. The in-plane elasticity of a monolayer formed at air-water interface by 1,2-dipalmitoyl- sn-glycero- 3-phosphocholine (DPPC) lipids was reduced in the presence of the ILs. The x-ray reflectivity studies on polymer supported lipid bilayer have shown the bilayer to shrink and correspondingly exhibit an increase in electron density. The presence of a certain mol\% of negatively charged lipid, 1,2-dipalmitoyl-rac-glycero-3-phospho-L-serine (DPPS), in DPPC mono- and bi-layers enhances the effect considerably. © 2018 Elsevier B.V.