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The binding of linear diamine counterions with different methylene chain lengths to the amino-acid-based surfactants undecanoic L-isoleucine (und-IL) and undecanoic L-norleucine (und-NL) was investigated with NMR spectroscopy. The counterions studied were 1,2-ethylenediamine, 1,3-diaminopropane, 1,4-diaminobutane, 1,5-diaminopentane, and 1,6-diaminohexane. These counterions were all linear diamines with varying spacer chain lengths between the two amine functional groups. The sodium counterion was studied as well. Results showed that when the length of the counterion methylene chain was increased, the surfactants’ critical micelle concentrations (CMC) decreased. This decrease was attributed to diamines with longer methylene chains binding to multiple surfactant monomers below the CMC and thus acting as templating agents for the formation of micelles. The entropic hydrophobic effect and differences in diamine counterion charge also contributed to the size of the micelles and the surfactants’ CMCs in the solution. NMR diffusion measurements showed that the micelles formed by both surfactants were largest when 1,4-diaminobutane counterions were present in the solution. This amine also had the largest mole fraction of micelle-bound counterions. Finally, the und-NL micelles were larger than the und-IL micelles when 1,4-diaminobutane counterions were bound to the micelle surface. A model was proposed in which this surfactant formed non-spherical aggregates with both the surfactant molecules’ hydrocarbon chains and n-butyl amino acid side chains pointing toward the micelle core. The und-IL micelles, in contrast, were smaller and likely spherically shaped.