In this paper, the related concepts of fingerprint recognition technology and PKI are introduced at first. In the traditional identity authentication based on PKI, the shortage of "password + certificate" which is used to perform the identity authentication is analyzed. And combined with the process of fingerprint recognition, an E-commerce identity authentication system based on fingerprint recognition and PKI is put forward. This system performs the identity authentication with the method of "fingerprint + certificate". Then the trust chain with the personal source spot is established and solves the credibility problem of the users’ identity in E-commerce.