A highly selective electrochemiluminescent biosensor for the detection of target nephrotoxic toxin, ochratoxin A (OTA), was developed using a DNA aptamer as the recognition element and N-(4-aminobutyl)-N-ethylisoluminol (ABEI) as the signal-producing compound. The electrochemiluminescent aptamer biosensor was fabricated by immobilizing aptamer complementary DNA 1 sequence onto the surface of a gold-nanoparticle (AuNP)-modified gold electrode. ABEI-labeled aptamer DNA 2 sequence hybridized to DNA 1 and was utilized as an electrochemiluminescent probe. A decreased electrochemiluminescence (ECL) signal was generated upon aptamer recognition of the target OTA, which induced the dissociation of DNA 2 (ABEI-labeled aptamer electrochemiluminescent probe) from DNA 1 and moved it far away from the electrode surface. Under the optimal conditions, the decreased ECL intensity was proportional to an OTA concentration ranging from 0.02 to 3.0 ng mL(-1), with a detection limit of 0.007 ng mL(-1). The relative standard deviation was 3.8% at 0.2 ng mL(-1) (n = 7). The proposed method has been applied to measure OTA in naturally contaminated wheat samples and validated by an official method. This work demonstrates the combination of a highly binding aptamer with a highly sensitive ECL technique to design an electrochemiluminescent biosensor, which is a very promising approach for the determination of small-molecule toxins.