The construction of an ultrasensitive, reagentless, target label free electrochemical aptamer sensor (aptasensor) for thrombin detection is described. The aptasensor is based on a chronoamperometric beacon system for biomolecular recognition. The ferrocene-labeled aptamer adopts a 3-D conformational change when interacts with thrombin. Thus the ferrocene label is approached to the microperoxise-11 (MP-11) attached on the electrode surface. The thrombin–aptamer interaction is detected via a microperoxidase mediated electron transfer between the ferrocene and the surface. This system was demonstrated with surface plasmon resonance, impedance spectroscopy and chronoamperometry measurements, obtaining higher sensitivity (30 fM) with impedance spectroscopy.