Molecular interaction of a self-assembling peptide, EAK16-II, to single- and double-stranded oligodeoxynucleotides (ODNs) was investigated under various solution conditions. The molecular events leading to EAK-ODN complexation and further aggregation were elucidated using a series of spectroscopic and microscopic methods. Despite the ability to self-assemble, EAK molecules bind to ODN molecules first upon mixing, resulting in EAK-ODN complexes. The complexes further associate to form EAK-ODN aggregates. A method based on UV-Vis absorption and centrifugation was developed to quantify the fraction of ODNs in the aggregates. The results were used to construct binding isotherms via a binding density function analysis. To compare the effects of different pH values and nucleotide types, the modified noncooperative McGhee and von Hippel model was used to extract binding parameters from the binding isotherms. The binding constant of EAK to ODNs was higher at pH 4 than at pH 7, and no binding was observed at pH 11, indicating that the interaction involved is primarily electrostatic in nature. EAK bound more strongly to single-stranded ODNs. The EAK-ODN aggregates were further visualized using atomic force microscopy; their size distribution as a function of EAK concentration was monitored by dynamic light scattering. The timescale for the EAK-ODN aggregation was on the order of minutes by fluorescence anisotropy and steady-state light scattering experiments. Fluorescence quenching experiments demonstrated that the ODNs in the aggregates were less accessible to the solvent, demonstrating a potential of oligonucleotide encapsulation by the self-assembling peptide.