Aptamers are short DNA or RNA oligonucleotides that can bind with high affinity and specificity to a wide spectrum of targets, including small molecules, proteins, and cells. Therefore aptamers have been widely used as new molecular recognition and detection ligands for various molecular targets. Herein, a novel label-free electrochemical IgE aptasensor based on direct immobilization of the redox probes on a composite electrode surface was reported. Glassy carbon electrode coated with the robust nanocomposite containing multiwalled carbon nanotube (MWCNTs)/ionic liquid (IL) 1-buthylmethylpyrolydinium bis (trifluromethyl sulfonyl) imide [C4mpyr][NTf2] and chitosan. At first the composite of chitosan and room temperature ionic liquid was modified with thionine (Th) through the covalence bond by a linker. Then the relative IgE aptamer covalantly attached to the thionine. The thionine act as molecular wire and allow the electrochemical communication with an otherwise of electrode. The aptamer was used as receptor-ligand model systems which specifically bind to the IgE.