Restriction site-associated DNA sequencing (RAD-seq) enables obtaining thousands of genetic markers for phylogenomic studies. However, RAD-seq data are subject to allele dropout (ADO) due to polymorphisms at enzyme cutting sites. We developed a new pipeline, RADADOR, to mitigate the ADO in outgroups by recovering missing loci from previously published transcriptomes in our study of a gymnosperm genus Torreya. Using the supplemented RAD-seq data in combination with plastome and mitochondrial gene sequences, morphology, and fossil records, we reconstructed the phylogenetic and biogeographic histories of the genus and test hypotheses on diversity anomaly in eastern Asian-North American floristic disjunction. Our results showed that our pipeline recovered many loci missing from the outgroup, and the improved data yielded a more robust phylogeny for Torreya. Using the fossilized-birth-death model and divergence-extinction-cladogenesis method we resolved detailed biogeographic history of Torreya that suggested a Jurassic origin in the Laurasia and differential speciation and extinction among continents accounting for the modern diversity anomaly biased toward Eastern Asia (EA). The history also supported a vicariance origin of the modern Torreya from a widespread ancestor in EA and NA in the mid-Eocene, cross-Beringia exchange in the early Paleogene before the vicariant isolation, in contrast to the “Out of NA” pattern common to gymnosperms and in contrast to the “Out of EA” hypothesis previously proposed for the genus. Furthermore, we observed phylogenetic discordance between the nuclear and plastid phylogenies on T. jackii, suggesting differential lineage sorting of plastid genomes among Torreya species or plastid genome capture in T. jackii.