The effect of two monovalent salts differing in the anions (sodium acetate and sodium chloride) on intermolecular aggregation of fully protonated hydrophobically modified (HM) chitosan in dilute aqueous solutions was studied by light scattering. It was demonstrated that both salts promote the aggregation of similarly charged macromolecules. At the same time, strong ion specificity is observed: acetate ions induce the growth of the aggregates, whereas chloride ions increase the fraction of aggregated chains. The behavior observed was attributed to different mechanisms of interactions of these ions with HM chitosan. Acetate ions possessing higher affinity to chitosan involving electrostatic and hydrophobic interactions as well as hydrogen bonding screen more effectively the electrostatic repulsion between polycationic chains, which allows accommodating more macromolecules within one aggregate. On the other hand, more compact chloride ions seem to promote the formation of crystalline zones within the aggregates, thereby increasing the association energy in the system. This provides a higher fraction of associated chains, whereas keeping a small aggregation number, because large amount of macromolecules in one aggregate can hinder sterically a proper mutual arrangement of the chains necessary for the formation of crystallites.