Traffic classification is key for managing both QoS and security in the Internet of Things (IoT). However, new traffic obfuscation techniques have been developed to thwart classification. Traffic mutation is one such obfuscation technique, that consists of modifying the flow’s statistical characteristics to mislead the traffic classifier. In fact, this same technique can also be used to hide normal traffic characteristics for the sake of privacy. However, the concern is its use by attackers to bypass intrusion detection systems by modifying the attack traffic characteristics. In this paper, we propose an unsupervised Deep Learning (DL)-based model to detect mutated traffic. This model is based on generative DL architectures, namely Autoencoders (AE) and Generative Adversarial Network (GAN). This model consists of a denoising AE to de-anonymize the mutated traffic and a discriminator to detect it. The implementation results show that the traffic can be denoised when different mutation techniques are applied with a reconstruction error less than $$10^{-1}$$. In addition, the detection rate of fake traffic reaches 83.7%.