Although cationic biocides have been used as membrane active biocides which attack the integrity or the function of the cytoplasm membrane over 40 years, the precise molecular interactions between bacterial cells and cationic biocides have not been fully discovered. It is generally believed that the electrostatic interaction between positively charged cationic biocides and negatively charged microbial surfaces attract cationic biocides to the surfaces and then the hydrophobic alkyl chains interfere with the cell membrane leading to the death of cells. Numerous researchers have reported that an increase of alkyl chain significantly enhances the antimicrobial activity of cationic biocides. Confusingly it was also reported that the antimicrobial ability was not influenced by the alkyl chain length. In their model, cationic biocides interfere with the other positively charged divalent metallic cations such as Ca2+ and Mg2+ which are very important to maintain the membrane integrity, and participate in the signal transduction and the enzymatic activity. Therefore the second objective of this study is to further investigate the correlation between the antibacterial efficiency and the structure of pCBAA derivatives and cationic polymers. S. epidermidis and E. coli K12 were used as the model bacteria for gram-positive and gram-negative bacteria. pCBAA derivatives with different structure and cationic polymers with different length of alkyl chain were tested in this study. Cationic polymer with shortest alkyl chain is able to kill both bacterial strains, and the antimicrobial efficiency increases with the increase of hydrophobic moieties of pCBAA derivatives and cationic polymers. In this work, dynamic light scattering were utilized to study the interactions between cationic compounds with different structure and bacterial membranes, and the results show that the cationic compounds carrying more hydrophobic moities showed higher binding affinity with bacterial cells. This result suggested that the long alkyl chain is not necessary for cationic compounds to kill bacterial but can improve the antimicrobial efficiency of cationic polymers.