Many organisms including mammalians use Antimicrobial Peptides (AMPs) which are also called Host Defense Peptides against microbial organisms. AMPs are among one of the ancient and successful strategies for both plant and animal kingdoms. Even though AMPs vary among closely related species and despite they have different sequences, many of the natural AMPs share similar properties. They are mostly short sequenced, structurally amphipathic and they carry overall net positive charge. Cationic AMPs target bacterial membranes because of the electrostatic attractions between positively charged peptides and negatively charged membranes. Due to the electrostatic attractions, cationic AMPs might work on membrane disruption by passing a certain threshold concentration for hydrophobic groups to penetrate into membrane. Noncovalent interactions and electrostatic interactions can create molecular attractions and may cause molecular self-assembly which is a common mechanism used by nature for several tasks. Self-assembling peptide amphiphiles are a group of molecules which can form nanofibrous structures and may contain bioactive epitopes depending on the target of the peptide amphiphile molecule. This thesis describes the presentation of antimicrobial sequences on supramolecular nanofibers which are formed by self-assembling peptides. The comparison of self-assembling peptides and single soluble peptides without self-assembling capacity, resulting significant improvement for peptide nanofiber systems for antimicrobial therapeutic purposes is reported.