Emotion regulation is a complex cognitive ability wherein conscious or non-conscious processes in an individual result in a change of experienced affect. The work in this dissertation involves advanced fMRI analyses to elucidate the connectivity of the neurobiological mechanisms of emotion regulation. We investigate the temporality of activation and functional connectivity in a form of explicit emotion regulation (cognitive reappraisal), as well as the effective connectivity of a form of implicit emotion regulation (affect labeling). We also investigate resting state functional connectivity in a subset of the emotion regulation network. Finally, these approaches are applied to euthymic individuals with bipolar disorder, a serious psychiatric illness in which the ability to regulate emotion is a cyclical and fundamental difficulty. The aim of this work is to identify system-level biomarkers to someday assist the diagnostic process and the tracking and treatment of therapeutic interventions.