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Backdoor attacks have been shown to be a serious threat against deep learning systems such as biometric authentication and autonomous driving. An effective backdoor attack could enforce the model misbehave under certain predefined conditions, i.e., triggers, but behave normally otherwise. The triggers of existing attacks are mainly injected in the pixel space, which tend to be visually identifiable at both training and inference stages and detectable by existing defenses. In this paper, we propose a simple but effective and invisible black-box backdoor attack FTROJAN through trojaning the frequency domain. The key intuition is that triggering perturbations in the frequency domain correspond to small pixel-wise perturbations dispersed across the entire image, breaking the underlying assumptions of existing defenses and making the poisoning images visually indistinguishable from clean ones. Extensive experimental evaluations show that FTROJAN is highly effective and the poisoning images retain high perceptual quality. Moreover, we show that FTROJAN can robustly elude or significantly degenerate the performance of existing defenses.