Simple yet efficient detection methods for food allergens are in urgent need to help people avoid the risks imposed by allergenic food. In this work, a polydopamine (PDA)-based fluorescent aptasensor was developed to detect arginine kinase (AK), one of the major allergens in shellfish. The aptamer towards AK was firstly selected via systematic evolution of ligands by exponential enrichment method and labeled with fluorescein amidite (FAM) to build a fluorescence resonance energy transfer (FRET) system with PDA particles. Polyethylene glycol (PEG) was employed to construct an antifouling surface for the aptasensor to eliminate food matrix interferences. With the presence of AK, the PDA-based aptasensor exhibited elevated fluorescent signals as the FAM-labeled aptamer bound to AK and detached from the PDA particles. The aptasensor showed great stability and resistance to nonspecific interference of background proteins and had a limit of detection (LOD) of 0.298 μg/mL. The proposed aptasensor was further proved to be feasible for quantitative analysis of AK in nine species of shrimps and five commercial processed products, which indicated its high potential in tracing the presence of AK in complex aquatic products.