| Summary: | <i>Ormosia</i> is a genus of the Fabaceae family that shows a distinct evolutionary history due to its typical Asian-American tropical disjunction distribution pattern. However, both its phylogeny and biogeographic mechanisms have not been fully resolved. In addition, <i>Ormosia</i> species have great economic and ecological potential in the wood and handicraft (using their attractive seeds) industries, reforestation, and folk medicine (due to their flavonoids, alkaloids, and terpenoids), making them highly valuable in research, especially from a genomic perspective. We report the genome assemblies of two common <i>Ormosia</i> species, <i>Ormosia emarginata</i> and <i>Ormosia semicastrata</i>, in South China, using both long and short sequencing reads. The genome assemblies of <i>O. emarginata</i> and <i>O. semicastrata</i> comprised 90 contigs with a total length of 1,420,917,605 bp and 63 contigs with a total length of 1,511,766,959 bp, respectively. Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment revealed 97.0% and 98.3% completeness of the <i>O. emarginata</i> and <i>O. semicastrata</i> assemblies, respectively. The assemblies contain 48,599 and 52,067 protein-coding genes, respectively. Phylogenetic analyses using 1032 single-copy genes with 19 species indicated that they are closely related to <i>Lupinus albus</i>. We investigated genes related to plant hormones, signaling, the circadian rhythm, transcription factors, and secondary metabolites derived from the whole genome and tandem and proximal duplications, indicating that these duplications should play important roles in the growth, development, and defense of <i>Ormosia</i> species. To our knowledge, our study is the first report on <i>Ormosia</i> genome assemblies. This information will facilitate phylogenetic and biogeographic analyses and species breeding in the future.
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