Chronic hypervigilance, a state of sustained alertness and hyperarousal in the absence of threat, has been shown to predict poorer clinical outcomes post-trauma. An exaggerated and persistent amygdala alerting response to affective information has been proposed as a reactivity-based, and thus indirect, marker of hypervigilance. However, because chronic hypervigilance is a persistent rather than reactive state, it should be directly observable under resting-state conditions without the need for exposure to affectively charged stimuli. We tested resting amygdala connectivity and basal sympathetic and hypothalamic-pituitary-adrenal axis activity as direct neural and neuroendocrine markers of chronic hypervigilance. 24 trauma-exposed women (age M = 22.9, SD = 5.5) and 20 no-trauma controls (age M = 21.1, SD = 3.2). Amygdala connectivity was measured using functional magnetic resonance imaging at rest and during viewing of novel and familiar affective scenes. Elevated amygdala connectivity during the viewing of novel scenes (exaggerated alerting response) and familiar scenes (persistent alerting response) was used as a reactivity-based index of hypervigilance. Resting amygdala connectivity and basal salivary alpha-amylase (sAA) and cortisol were tested as neural and neuroendocrine markers of hypervigilance, respectively. Compared to no-trauma controls, trauma-exposed women showed greater connectivity between the left amygdala and the ventral anterior cingulate cortex (vACC) both during affective processing and at rest. Exaggerated neural novelty response was associated with greater resting left amygdala-vACC connectivity and higher basal sAA, but not cortisol. Greater synchronization of threat-detection circuitry in the absence of threat and basal sympathetic tone might serve as complementary resting-state markers of the cognitive and physiological components of chronic hypervigilance, respectively.