We report a virus-based biological template, M13 bacteriophage, for selecting single-walled carbon nanotubes’ (SWCNTs’) chirality, based on the premise that binding affinity between carbon nanotubes (CNTs) and peptides are sensitive to amino acid sequences. Bacteriophage pIII capsid fusion peptides, which have high binding affinity for CNTs, were identified through an evolutionary screening process by a phage display technique. Most of the binding sequences are rich in aromatic amino acids, begin with histidine, and possess hydrophobic properties. Direct evidence of binding was provided by the attachment of SWCNTs to selected bacteriophage-coated microspheres via an anti-M13 monoclonal antibody and by the attachment of CdTe quantum dots coupled with the selected peptides to SWCNTs. Efficient dispersion of debundled SWCNTs was achieved by the selected peptides whose conformation is characterized by circular dichroism. Quantitative analysis of the binding affinity was carried out using molecular dynamics simulations, demonstrating that the best binder, HESFWYLPHQSY, has the highest binding energy with (7, 6) SWCNT in the peptide pool. Computational calculations also show that the selected peptides preferentially bind to large-diameter tubes and the peptide HSNWRVPSPWQL has the best discernment on chirality. Chiral selectivity was examined by UV-vis-NIR and photoluminescence spectroscopy, showing that HSNWRVPSPWQL could shift the SWCNT size distribution to larger diameter and enrich (10, 3), (9, 5), (12, 2), (11, 4), and (10, 6). This work presents chirality-preferential dispersion of SWCNTs by phage-displayed peptides for the first time, and offers new prospects of understanding the mechanism of peptide–CNT binding and producing “designer” peptide for CNT surface recognition.