An aptamer-based assay is presented for the determination of fumonisin B1 (FB1). It is bimodal in that both surface-enhanced Raman spectroscopy (SERS) and fluorometry are applied for quantitation. It makes use of platinum-coated gold nanorod (AuNR) and DNA sequences. The complementary DNA of aptamer (cDNA) against FB1 is immobilized on the surface of AuNR. The aptamer of FB1 modified with Cy5.5 are complementarily hybridized with cDNA. In the absence of FB1, the aptamer and its cDNA associate. In this situation, strong SERS and weak fluorescence signals are obtained. In the presence of FB1, the aptamer disassociates with its cDNA and binds the target. As the concentration of FB1 increases, the SERS and fluorescence signal intensities of the mixture are gradually decreased and increased, respectively. Under optimized conditions, the SERS signal at 1366 cm−1 decreases linearly in the 10–500 pg mL−1 concentration range with the calibration equation of y = 1997lgx-594 (the coefficient of determination is 0.998). The fluorescence signal at 670 nm increases linearly in the 10–250 pg mL−1 concentration range with the calibration equation of y = 500lgx-383 (the coefficient of determination is 0.991). The assay was applied to the determination of FB1 contents in spiked corn samples. The average recoveries ranged from 92 to 107%, confirming the practicality of this method. The results obtained by this assay are in good agreement with that of LC-MS/MS method. Graphical abstractSchematic illustration of a bimodal aptasensor based on surface enhanced Raman scattering (SERS) and fluorescence change for the detection of fumonisin B1 (FB1).