In this paper, a multilayer security solution is introduced, in order to accord the required end-to-end security blanket to the heterogeneous networks by considering the properties used by authentication at the physical-layer in transport-layer authentication. In particular, after achieving an authentication level based on the estimated channel impulse response (CIR) at the physicallayer, these CIRs are exploited at the transport layer, adding more randomness to the generated sequence numbers used in the 3-Way TCP/IP handshake authentication. Furthermore, in order to enhance the authentication at the physical layer, the estimated CIR is quantized into two domains: amplitude and phase. The quantizer’s output is used to differentiate between the legitimate transmitters and intruders using binary hypothesis testing. Eventually, generating a unique sequence numbers is granted due to the increased randomness offered by the quantizer outputs. In order to verify the effectiveness of the proposed scheme, simulation results are shown based on an orthogonal frequency division multiplexing (OFDM) system. Additionally, a logarithmic likelihood ratio test is used to evaluate the authentication performance.