Fingerprint recognition or fingerprint authentication refers to the automated method of verifying a match between two human fingerprints. Fingerprints are one of many forms of biometrics used to identify individuals and verify their identity. Also Face recognition becomes one of the popular biometric identification systems used in identifying or verifying individuals and matching it against library of known faces. Also it finds its application in wide variety of areas like criminal identification, human - computer interaction, security systems, credit- card verification, teleconference, image and film processing. They are fused together by score level fusion. Score level fusion is a method in which the weights of multiple Biometric features are compared against the images in the database and a new weight will be generated. If the weight is above threshold, then the user will be recognized and the first level of authentication will be completed. The second level of authentication for a user is done using One Time Password. But normally these are just random numbers that can be easily judged and hence may pose threat to some sensitive information. As a solution for this problem, the scheme proposed in this paper makes use of Elliptic Curve Cryptography, a public key cryptographic method, to generate One Time Password. As Elliptic Curve Cryptography is a strong asymmetric algorithm it is difficult to hack them in the reverse direction due to computational complexity and the uniqueness of the final fused weight value that is used as private key. Hence this proposed system is more reliable than any other conventional systems.