The objective of this study was to develop a simple and rapid method that could detect and discriminate four specific pesticides (isocarbophos, omethoate, phorate, and profenofos) using a single aptamer-based capture procedure followed by Surface Enhanced Raman Spectroscopy (SERS). The aptamer is a single stranded DNA sequence that is specific to capture these four pesticides. The thiolated aptamer was conjugated onto silver (Ag) dendrites, a nanostructure that can enhance the Raman fingerprint of pesticides, through Ag–thiol bonds. It was then backfilled with 6-mercaptohexanol (MH) to prevent nonspecific binding. The modified SERS platform [Ag–(Ap + MH)] was then mixed with each pesticide solution (P) for 20 min. After capturing the pesticides, the Ag–(Ap + MH)–P complex was analyzed under a DXR Raman microscope and TQ Analyst software. The results show that the four pesticides can be captured and detected using principal component analysis based on their distinct fingerprint Raman peaks. The limits of detection (LODs) of isocarbophos, omethoate, phorate, and profenofos were 3.4 μM (1 ppm), 24 μM (5 ppm), 0.4 μM (0.1 ppm), and 14 μM (5 ppm) respectively. This method was also validated successfully in apple juice. These results demonstrated the super capacity of aptamer-based SERS in rapid detection and discrimination of multi-pesticides. This technique can be extended to detect a wide range of pesticides using specific aptamers.