Mood disorders, anxiety disorders and borderline personality disorder overlap in symptom criteria, are highly comorbid with one another, and group together in factor models of psychopathology (Kotov et al., 2011). These disorders of emotional distress are characterized by increased frequency and duration of intense negative affect, large abrupt shifts in affect (i.e., affective instability), and behavioral dysregulation (Selby, Anestis, Bender, and Joiner, 2009). Functional connectivity between the amygdala and the ventromedial prefrontal cortex (vmPFC) has been proposed as a possible endophenotype for emotion dysregulation. However, the relationship between amygdala-vmPFC connectivity and transdiagnostic symptoms of emotional distress is largely unknown. The present study used two powerful methodologies, fMRI and Ecological Momentary Assessment, to examine the relationship between amygdala-vmPFC resting state functional connectivity (rs-FC) and dysregulated moods and behaviors in daily lives. Twenty-seven women in treatment for a disorder of emotional distress completed clinical interviews, self-report questionnaires on symptoms and emotion regulation, resting state scans, and two weeks of frequent surveys assessing moods and behaviors. Results found that amygdala-vmPFC rs-FC was (a) correlated with frequency of behavioral dysregulation, including drinking alcohol to cope with distress, binge eating, and impulsivity, and (b) differentially correlated with anxiety and depression, replicating the results of previous research (Burghy et al., 2012). Results also found that another emotion circuit, the dACC-amygdala, was associated with negative affect and affective instability. The current research found evidence for neural mechanisms related to emotional and behavioral dysregulation in daily lives of women with transdiagnostic disorders of emotional distress.