The ability to selectively perceive items in the environment may be modulated by the emotional content of those items. The neural mechanism that underlies the privileged processing of emotionally salient content is poorly understood. Here, using fMRI, we investigated this issue via a binocular rivalry procedure when face stimuli depicting fearful or neutral expressions competed for awareness with a house. Results revealed an interesting dissociation in the amygdala during rivalry condition: Whereas its dorsal component exhibited dominant activation to aware fearful faces, a ventral component was more active during the suppression of fearful faces. Moreover, during rivalry, the dorsal and ventral components of the amygdala were coupled with segregated cortical activations in the brainstem and medial PFC, respectively. In summary, this study points to a differential involvement of two clusters within the amygdala and their connected networks in naturally occurring perceptual biases of emotional content in faces.