Recently, major progress has been made towards the realisation of quantum internet to enable a broad range of classically intractable applications. These applications such as delegated quantum computation require running a secure identification protocol between a low-resource and a high-resource party to provide secure communication. In this work, we propose two identification protocols based on the emerging hardware secure solutions, the quantum Physical Unclonable Functions (qPUFs). The first protocol allows a low-resource party to prove its identity to a high-resource party and in the second protocol, it is vice-versa. Unlike existing identification protocols based on Quantum Read-out PUFs which rely on the security against a specific family of attacks, our protocols provide provable exponential security against any Quantum Polynomial-Time adversary with resource-efficient parties. We provide a comprehensive comparison between the two proposed protocols in terms of resources such as quantum memory and computing ability required in both parties as well as the communication overhead between them.