Dispersal shapes demographic processes and therefore is fundamental to understanding biological, ecological, and evolutionary processes acting within populations. However, assessing population connectivity in scoters (Melanitta sp.) is challenging as these species have large spatial distributions that span remote landscapes, have varying nesting distributions (disjunct vs. continuous), exhibit unknown levels of dispersal, and vary in the timing of the formation of pair bonds (winter vs. fall/spring migration) that may influence the distribution of genetic diversity. Here, we used double‐digest restriction‐associated DNA sequence (ddRAD) and microsatellite genotype data to assess population structure within the three North American species of scoter (black scoter, M. americana; white‐winged scoter, M. deglandi; surf scoter, M. perspicillata), and between their European congeners (common scoter, M. nigra; velvet scoter, M. fusca). We uncovered no or weak genomic structure (ddRAD Φ_ST < 0.019; microsatellite F_ST < 0.004) within North America but high levels of structure among European congeners (ddRAD Φ_ST > 0.155, microsatellite F_ST > 0.086). The pattern of limited genomic structure within North America is shared with other sea duck species and is often attributed to male‐biased dispersal. Further, migratory tendencies (east vs. west) of female surf and white‐winged scoters in central Canada are known to vary across years, providing additional opportunities for intracontinental dispersal and a mechanism for the maintenance of genomic connectivity across North America. In contrast, the black scoter had relatively elevated levels of divergence between Alaska and Atlantic sites and a second genetic cluster found in Alaska at ddRAD loci was concordant with its disjunct breeding distribution suggestive of a dispersal barrier (behavioral or physical). Although scoter populations appear to be connected through a dispersal network, a small percentage (<4%) of ddRAD loci had elevated divergence which may be useful in linking areas (nesting, molting, staging, and wintering) throughout the annual cycle.