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Polymorphic gates are reconfigurable devices that deliver multiple functionalities at different temperature, supply voltage or external inputs. Capable of working in different modes, polymorphic gate is a promising candidate for embedding secret information such as fingerprints. In this paper, we report five polymorphic gates whose functionality varies in response to specific control input and propose a circuit fingerprinting scheme based on these gates. The scheme selectively replaces standard logic cells by polymorphic gates whose functionality differs with the standard cells only on Satisfiability Don’t Care conditions. Additional dummy fingerprint bits are also introduced to enhance the fingerprint’s robustness against attacks such as fingerprint removal and modification. Experimental results on ISCAS and MCNC benchmark circuits demonstrate that our scheme introduces low overhead. More specifically, the average overhead in area, speed and power are 4.04%, 6.97% and 4.15% respectively when we embed 64-bit fingerprint that consists of 32 real fingerprint bits and 32 dummy bits. This is only half of the overhead of the other known approach when they create 32-bit fingerprints.