Abstract: Peptides rich in basic residues such as lysine and arginine play important roles in biology such as bacterial defense and cell penetration. Although peptide-binding materials with high sequence specificity have broad potential applications, the diverse functionalities of peptide side chains make their molecular recognition extremely difficult. By covalently capturing micelles of a doubly cross-linkable surfactant with solubilized peptide templates, we prepared water-soluble molecularly imprinted nanoparticles with high sequence specificity for basic peptides. The nanoparticles interact with the side chains of lysine and arginine through hydrogen bonds strengthened by the nonpolar environment of the micelle. They have hydrophobic pockets in their core complementary to the hydrophobic side chains in size and shape. These recognition sites allowed the micelles to bind basic biological peptides strongly in water, with tens to hundreds of nanomolar in binding affinity