Liriodendron, once widespread during the early and middle Miocene, developed a disjunct distribution between East Asia and North America in the late Miocene due to environmental changes and land bridge ruptures. Understanding plant origin centers is vital for grasping biodiversity, adaptation, and evolution. Single copy orthologue sequences, inherited with low mutation rates and stable across generations, serve as ideal markers for studying population evolution. In this study, three stress related single copy genes (LtDHN2, LtDHN3, and LtTLP11) were cloned and sequenced in 29 Liriodendron populations. The gDNA datasets of LtDHN2, LtDHN3, and LtTLP11 contained 206, 1477, and 75 polymorphic sites, respectively, with most genetic differences between L. chinense and L. tulipifera, moderate individual differences within populations, and the least among populations within species. Both L. tulipifera and the eastern and western populations of L. chinense acted as ancestral populations, with historical gene flow between each pair. The divergence between L. chinense and L. tulipifera occurred approximately 11.4-13.3 million years (Ma) ago, with the eastern and western populations of L. chinense tracing their ancestry back to around 2.19-2.48 Ma. The effective population sizes of L. chinense expanded rapidly during 0.25–1.0 Ma and 0.5–1.5 Ma, while L. tulipifera expanded between 0.25–0.75 Ma and 0.5–2.5 Ma, coinciding with Quaternary glaciations that significantly impacted temperate flora distribution and diversity in East Asia and North America. Understanding the historical and current genetic diversity of Liriodendron species provides molecular evidence for their origins and guides the utilization of their germplasm resources.