Molecular organization in surface monolayers, aqueous bilayers and related systems provides unique advantages for molecular recognition. Monomolecular layers on water are capable of conplementary hydrogen bonding with aqueous guests in spite of surrounding bulk water. This feature was applied to multi-site recognition of mixed monolayers and template-directed molecular patterning. Specific peptide-peptide interaction is also a result of this unique interfacial feature. Effective hydrogen bonding at the macroscopic air-water interface is much reduced at the microscopic interface of micelles and vesicles. The alternate adsorption of linear polyions was extended to globular proteins and a large variety of designed protein/polyion layers were produced.