Orychophragmus violaceus, referred to as “eryuelan” (February orchid) in China, is an early-flowering ornamental plant. The high oil content and abundance of unsaturated fatty acids in O. violaceusseeds make it a potential high-quality oilseed crop. Here, we generated a whole-genome assembly for O. violaceususing Nanopore and Hi-C sequencing technologies. The assembled genome of O. violaceuswas ∼1.3 Gb in size, with 12 pairs of chromosomes. Through investigation of ancestral genome evolution, we determined that the genome of O. violaceusexperienced a tetraploidization event from a diploid progenitor with the translocated proto-Calepineae karyotype. Comparisons between the reconstructed subgenomes of O. violaceusidentified indicators of subgenome dominance, indicating that subgenomes likely originated via allotetraploidy. O. violaceuswas phylogenetically close to the Brassicagenus, and tetraploidy in O. violaceusoccurred approximately 8.57 million years ago, close in time to the whole-genome triplication of Brassicathat likely arose via an intermediate tetraploid lineage. However, the tetraploidization in Orychophragmuswas independent of the hexaploidization in Brassica, as evidenced by the results from detailed phylogenetic analyses and comparisons of the break and fusion points of ancestral genomic blocks. Moreover, identification of multi-copy genes regulating the production of high-quality oil highlighted the contributions of both tetraploidization and tandem duplication to functional innovation in O. violaceus. These findings provide novel insights into the polyploidization evolution of plant species and will promote both functional genomic studies and domestication/breeding efforts in O. violaceus.