In covalent polymerization, a single monomer can result in different polymer structures due to positional, geometric, or stereoisomerism. We demonstrate that strong hydrophobic interactions result in stable noncovalent polymer isomers that are based on the same covalent unit (amphiphilic perylene diimide). These isomers have different structures and electronic/photonic properties, and are stable in water, even upon prolonged heating at 100 8C. Such combination of covalent-like stability together with structural/functional variation is unique for noncovalent polymers, substantially advancing their potential as functional materials.