In order to solve such problems as low-level security of traceability code for agricultural products and difficulty to guarantee the traceability code was unique for one product, taking aquatic products as research object, an encryption algorithm of traceability code for aquatic products was put forward. At the base of analysis to coding solution of traceability code and AES encryption algorithm, the aquatic product was coded. Then, this supervision code was compressed and encrypted by an algorithm namely decimal and equal-length to generate the traceability code for aquatic products. The experimental results showed that the proposed algorithm was feasible and reliable. It ensured the deployment security of traceability system owing to the feature of uniqueness and dynamic cipher of traceability code. An example of the application solution of the encryption algorithm in aquatic products traceability system was introduced. 