The Pleistocene glaciations represent the most recent and dramatic series of habitat changes since the Cretaceous. The impact of these events was particularly acute for aquatic taxa with poor powers of dispersal, but few organisms have evolutionary histories more intimately entwined with the advance and retreat of ice than the ‘glacial relicts’. In this study, we used a mitochondrial gene, cytochrome c oxidase subunit I (COI), to examine and compare the phylogeographical structure of two glacial relict crustaceans (Limnocalanus macrurus and members of the Mysis relicta species group) across North America. In both cases, we found a sharp phylogenetic division between populations from inland lakes formed during glacial retreat, and arctic lakes isolated from polar seas via isostatic rebound. However, the depth of this phylogenetic partition varied between taxa. In L. macrurus, nucleotide sequence divergence of 2.2% between these zones is consistent with its current status as a single morphologically variable species, but in Mysis the split occurred among recently described, morphologically conserved species, at a divergence of 8.2%. The disparity in the depth of divergence indicates a history of recurrent freshwater invasions from the arctic seas, in concordance with previous studies of Eurasian glacial relicts. However, we suggest further consideration of a largely overlooked explanation that could account for some of the discrepancies between molecular divergences and glaciation events. Many cladogenetic events could have occurred in arctic seas prior to the transition to inland waters, a possibility supported both by the complex physical and ionic history of arctic seas and by high marine and estuarine lineage diversity in the north.