The inclusion complexation (IC) of between cationic poly(ε-lysine) (PL) chains and α-cyclodextrin (CD) molecules under varied conditions was reported. It was found that the ionization of the side groups control the threading of CD molecules. The analysis showed that the yield of PL ICs was significantly affected by the pH of aqueous media, due to the protonation of amino side groups of PL and the ionization of hydroxyl groups of α-CD.