Authentication of seafood is critical for ensuring consistent food quality. In the present study, amino acids (AAs) carbon stable isotope fingerprinting was investigated for its potential to identify sea cucumber (Apostichopus japonicus) from different geographical origins and different production methods. AA compositions and δ13CAA values of wild and cultured samples of A. japonicus from different sampling sites in China were determined by gas chromatography combustion isotope ratio mass spectrometry (GC-C-IRMS). Data obtained was analyzed by multivariate statistics including principal component analysis and linear discriminant analysis. These results showed that the AA compositions were identified samples from different sea areas and different production methods. AAs carbon stable isotope fingerprinting improved the identification, it discriminated samples from the different sampling sub-regions. An overall correct classification rate of 100.0% and a cross-validation rate of 100.0% were obtained for the eight A. japonicus sampling sub-regions based on δ13CAA values and compared to 100.0% and 100.0% for the wild samples and cultured samples. Thus, compound-specific isotope analysis (CSIA) of AAs represents a promising method for accurate identification of the geographic origins and production methods of A. japonicus in the coastal areas of China.