Recent studies have shown that deep neural networks (DNN) are vulnerable to various adversarial attacks. In particular, an adversary can inject a stealthy backdoor into a model such that the compromised model will behave normally without the presence of the trigger. Techniques for generating backdoor images that are visually imperceptible from clean images have also been developed recently, which further enhance the stealthiness of the backdoor attacks from the input space. Along with the development of attacks, defense against backdoor attacks is also evolving. Many existing countermeasures found that backdoor tends to leave tangible footprints in the latent or feature space, which can be utilized to mitigate backdoor attacks.In this paper, we extend the concept of imperceptible backdoor from the input space to the latent representation, which significantly improves the effectiveness against the existing defense mechanisms, especially those relying on the distinguishability between clean inputs and backdoor inputs in latent space. In the proposed framework, the trigger function will learn to manipulate the input by injecting imperceptible input noise while matching the latent representations of the clean and manipulated inputs via a Wasserstein-based regularization of the corresponding empirical distributions. We formulate such an objective as a non-convex and constrained optimization problem and solve the problem with an efficient stochastic alternating optimization procedure. We name the proposed backdoor attack as Wasserstein Backdoor (WB), which achieves a high attack success rate while being stealthy from both the input and latent spaces, as tested in several benchmark datasets, including MNIST, CIFAR10, GTSRB, and TinyImagenet.