The eastern Asia (EA) – eastern North America (ENA) disjunction is a typical and well known biogeographic. Although its origin has been the topic of many studies, some new insights will arise when more complex evolutionary histories are revealed using phylogenomic methods. Here, we used targeted exon capture and sequenced >1,000 single copy nuclear, plus 73 chloroplast genes, to resolve interspecific relationships and the biogeographic history of an intercontinental disjunct genus Thuja. Two separate clades were detected: the “EA clade” comprised two species (T. standishii and T. sutchuenensis) from EA, and the “disjunct clade” comprising T. koraiensis, T. occidentalis, and T. plicata, with the first two comprising an EA–ENA disjunct pattern and T. plicata in western North America. The disjunct clade experienced a rapid radiation in the Mid–Miocene, and furthermore multispecies coalescent analysis revealed that ancient lineages of Thuja had large population sizes. These two factors might have contributed to the significant levels of incomplete lineage sorting (ILS) we detected within Thuja, and especially the disjunct clade. Because of this, EA–ENA disjunct pattern of T. koraiensis and T. occidentalis is exhibited by only 13.98% of genes examined. In addition, we found that ~20% of the T. sutchuenensis nuclear genome is derived from an as–yet–unrecognized ancestral lineage of Thuja, which might explain the close resemblance of cone morphology between T. sutchuenensis and the Paleocene fossil species T. ehrenswaerdii. Overall, our study demonstrates that single genes may produce incomplete or inaccurate phylogenies for disjunct taxa, and that more accurate results will come from using genomic data, revealing a more complex evolutionary history. This will steadily improve our understanding of their origin and evolution.