The elimination of matrix interference is now a task for further development and application of immunoassays. Here the effect of proteins in aquatic samples on immunoassay was investigated by western blotting and competitive indirect enzyme-labeled immunosorbent assay (ci-ELISA). Some proteins in flatfishes interacted with different antibodies, resulting in significant loss of accuracy of the immunoassays. Moreover, these matrix proteins prefer to interact with enzyme-labeled antibodies than label-free ones. Such a matrix protein-immunoglobulin interaction was validated with different fish and shrimp samples and similar results were observed, which demonstrated a universal significance of the protein-induced matrix interference to immunoassays. Besides, the strategies to prevent such interference were preliminarily discussed.