Bacillus thuringiensis is a bacterium that produces many insecticidal proteins including cytolytic proteins or Cyt toxins. Although the Cyt toxin shows specific toxicity against Dipteran insect species, the toxin binds directly to the lipid membrane without a specific protein receptor requirement. In this work, we have investigated the interaction of Cyt2Aa2 toxin with lipid bilayers composed of different lipid phases. By means of atomic force microscopy (AFM), lipid phase separation was observed for 1:1 and 4:1 M mixtures of DPPC/POPC bilayers. The exposure of Cyt2Aa2 to these lipid bilayers revealed that the toxin selectively bound to Ld lipid bilayer (corresponding to POPC). In turn, it did not bind to the Lo and So phases (corresponding to DPPC). Interestingly, for the bilayer of 4:1 DPPC/POPC mixture, the binding of Cyt2Aa2 was localized at the lipid phase boundary instead of Ld domain as occurred for the 1:1 DPPC/POPC bilayer. In addition, quartz crystal microbalance with dissipation experiments confirmed AFM results. In particular, the measurements showed that amount of protein bound to 1:1 DPPC/POPC (with phase separation) was half of the binding quantified for the Ld phase lipid bilayer (pure POPC and 1:4 DPPC/POPC mixture). These results indicate that the lipid phase (lipid acyl chain) influences the Cyt2Aa2-lipid interaction.