A novel aptamer based nanobiosensor for label free detection of Ochratoxin A (OTA) was developed in the present study. Pencil graphite electrode (PGE) surfaces modified with transition metal oxides (MeOx) were used as a platform for immobilizing the 5 ' aminohexyl linked aptamer sequence representing Ochratoxin A via carbodiimide chemistry. After blocking the residual active surface with bovine serum albumin, aptasensors were incubated with OTA solution to monitor their interaction by Electrochemical Impedance Spectrometry (EIS) in the presence of 5 mM [Fe(CN)(6)](3-/4-) based on the electron transfer resistances (R-ct). Operational and solution parameters such as the type of metal oxide (MnOx, MoOx and WOx) and the technique used in their deposition step being cyclic voltammetry (CV) or pulsed deposition (PD) along with the aptamer concentration were optimized by comparing the EIS measurements, and the best performance was obtained with MnOx modified PGEs by PD technique. Selectivity of the designed aptasensor was detected by using Aflatoxin B1 and Zearalenone as nonspecific molecules and from the calibration curves, the limit of detection (LOD) was calculated as 0.03 nM.