BACKGROUND: Functional abnormalities, mostly involving functionally specialized subsystems, have been associated with disorders of emotion regulation such as bipolar disorder (BD). Understanding how independent functional subsystems integrate globally and how they relate with anatomical cortical and subcortical networks is key to understanding how the human brain's architecture constrains functional interactions and underpins abnormalities of mood and emotion, particularly in BD. METHODS: Resting-state functional magnetic resonance time series were averaged to obtain individual functional connectivity matrices (using AFNI software); individual structural connectivity matrices were derived using deterministic non-tensor-based tractography (using ExploreDTI, version 4.8.6), weighted by streamline count and fractional anisotropy. Structural and functional nodes were defined using a subject-specific cortico-subcortical mapping (using Desikan-Killiany Atlas, FreeSurfer, version 5.3). Whole-brain connectivity alongside a permutation-based statistical approach and structure-function coupling were employed to investigate topological variance in individuals with predominantly euthymic BD relative to psychiatrically healthy control subjects. RESULTS: Patients with BD (n = 41) exhibited decreased (synchronous) connectivity in a subnetwork encompassing frontolimbic and posterior-occipital functional connections (T > 3, p = .048), alongside increased (antisynchronous) connectivity within a frontotemporal subnetwork (T > 3, p = .014); all relative to control subjects (n = 56). Preserved whole-brain functional connectivity and comparable structure-function coupling among whole-brain and edge-class connections were observed in patients with BD relative to control subjects. CONCLUSIONS: This study presents a functional map of BD dysconnectivity that differentially involves communication within nodes belonging to functionally specialized subsystems-default mode, frontoparietal, and frontolimbic systems; these changes do not extend to be detected globally and may be necessary to maintain a remitted clinical state of BD. Preserved structure-function coupling in BD despite evidence of regional anatomical and functional deficits suggests a dynamic interplay between structural and functional subnetworks.