Provided is a fingerprint authentication system and a method of authentication. The fingerprint authentication system may have a configuration to analyze a reflection wave signal reflected at a surface of an object under examination or an internal of the object under examination by applying a wave signal from at least one of signal communication unit of a fingerprint sensor to the object under examination. In the method of authentication, the controller in the fingerprint authentication system may be configured to selectively perform a first step authentication to authenticate a shape of a fingerprint, and a second step authentication to detect internal biometric information of the object under examination.