A powerful polymeric protein sensor was constructed by microcontact imprinting taking advantage of the specific interaction between a bisphosphonate binding monomer and lysine/arginine residues on the surface of trypsin.Modern healthcare demands rapid and accurate detection of proteins/enzymes at the ultratrace level. Herein we present a molecularly imprinted capacitive sensor for trypsin, developed by microcontact imprinting. High affinity and selectivity was achieved by doping the prepolymerization mixture with a stoichiometric amount of methacrylamide-based bisphosphonate (BP) monomer. Taking advantage of the specific interaction between bisphosphonate binding monomers and lysine/arginine residues on the surface of trypsin, we have constructed a powerful polymeric sensor. The BP based sensor has the ability to recognize trypsin over other arginine-rich proteins, even in high ionic strength buffers with a sub-picomolar detection limit (pM). We believe that the combination of supramolecular chemistry, molecular imprinting and advanced instrumentation has a potential for future drug development and diagnostics that extends beyond biomolecular recognition.