A method for manufacturing an array plate for biomolecules includes coating a surface of a substrate with a hydrophobic material to form a hydrophobic layer having initial hydrophobic properties, etching the hydrophobic layer through an etch mask placed thereon to form a hydrophilic binding site, removing the etch mask, and processing the remaining region of the hydrophobic layer to recover the initial hydrophobic properties. A method for manufacturing a biochip using this array plate, includes processing the surface of the hydrophilic binding site of the array plate to increase an affinity of biomolecules to the hydrophilic binding site, and applying a solution containing biomolecules to the surface of the hydrophilic binding site.