The disjunct temperate rainforests of the Pacific Northwest of North America (PNW) are characterized by late-successional dominant tree species western redcedar (Thuja plicata) and western hemlock (Tsuga heterophylla). The demographics of these species, along with the PNW rainforest ecosystem in its entirety, have been heavily impacted by the geological and climatic changes the PNW has experienced over the last 5 million years, including mountain orogeny and repeated Pleistocene glaciations. These environmental events have ultimately shaped the history of these species, with inland segments potentially being extirpated during the Pleistocene glaciation. Here, we collect genomic data for both species across their ranges in order to develop multiple demographic models, each reflecting a different hypothesis on how the ecosystem dominant species may have responded to dramatic climatic change. Results indicate that inland and coastal populations in both species diverged an estimated ~2.5 million years ago and experienced a decrease in population size during glaciation, with a subsequent population expansion. Importantly, we found evidence for gene-flow between coastal and inland populations during the mid-Holocene. It is likely that intermittent migration in these species has prevented allopatric speciation. In conclusion, the combination of genomic data and population demographic inference procedures involving machine learning establish that populations of the ecosystem dominants Thuja plicata and Tsuga heterophylla persisted in refugia located in both the coastal and inland regions, with populations expanding and contracting in response to glacial cycles with occasional gene-flow.