We propose a stochastic memristor utilizing ultrathin native-SiOx films (∼2.7 nm) and dynamic Ag nanoclusters for constructing physical unclonable function (PUF) hardware. The atomically thin solid electrolyte allows for quantum-mechanical tunneling current at high resistance states, which exponentially increases the entropy between separated devices. This results in good uniformity (54.4%), uniqueness (53.7%), and reliability (98.75%) for the prototype native-SiOx mem-PUF array. Furthermore, the proposed device demonstrates reconfigurability for key refreshing and passes all 15 National Institute of Science and Technology (NIST) tests, verifying the high randomness of the generated bits. Overall, this work highlights the potential of the ultrathin native-SiOx memristor for PUF applications.