Understanding the processes of divergence and speciation, particularly in the presence of gene flow, is key to understanding the generation of biodiversity. We investigated divergence and gene flow in nine lineages of birds with a trans-Beringian distribution, including pairs of populations, subspecies, and species, using ultra-conserved elements (UCEs). We found that although these lineages spanned conditions from panmixia to fully isolated species, they were not smoothly distributed across this continuum, but formed two discontinuous groups: relatively shallow splits with gene flow between Asian and North American populations, no fixed SNPs, and lower divergence and relatively deeply split lineages with multiple fixed SNPs, higher divergence, and relatively low rates of gene flow. All eight lineages in which two populations were distinguishable shared the same divergence model, one with gene flow without a prolonged period of isolation, despite the diversity of lineages included which would not necessarily be expected to have responded in the same ways to the glacial-interglacial cycles of connection and isolation in Beringia. Despite correlation between our UCE-based estimates of gene flow and previous estimates of divergence from mitochondrial DNA, we found that discord prevails among divergence estimates from mtDNA, AFLPs, and UCEs. Together, these results highlight the role of gene flow in influencing divergence in these Beringian lineages and of the presence in this region of discontinuous patterns of divergence.