This paper deals with implementing a steganography based multi-modal biometric system. For this purpose, we construct a multi-biometrics system based on the face and iris recognition. Here, the feature vector of iris pattern is hidden in the face image. The recognition system is designed by the fuzzy-based Linear Discriminant Analysis(LDA), which is an expanded approach of the LDA method combined by the theory of fuzzy sets. Furthermore, we present a watermarking method that can embed iris information into face images. Finally, we show the advantages of the proposed watermarking scheme by computing the ROC curves and make some comparisons recognition rates of watermarked face images with those of original ones. From various experiments, we found that our proposed scheme could be used for establishing efficient and secure multi-modal biometric systems.