Hue Yellow Ochna, also known as Hoang Mai Hue, is a precious ornamental plant in Vietnam. Its distinctive beauty has been celebrated in a long history, poetry, and in numerous paintings. However, there have been few studies on the population structure or phylogenetic relationships of Hue Ochna. In this study, we conducted genetic diversity and phylogenetic analysis using the nrITS DNA and trnL-F cpDNA sequences of Hue Ochna. The plant samples were collected from various areas of Thua Thien Hue province. We used ITS1 and ITS4 primers for the ITS region and trnL and trnF primers for the trnL-F region. The obtained DNA sequences were edited using BioEdit programs. The MEGA 11.0 program was used for phylogenetic analysis and to detect genetic distances. For the trnL-F region, 20 Hue Ochna samples had the same sequence and similarity to Ochna integerrima at the level of 99.75%. For the ITS region, the mean nucleotide composition was determined as 19.04% A, 34.6% C, 33.28% G, and 13.08% T. It was also found that divergence values differed between 0.000 and 0.014. The phylogenetic tree consisted of two large branches. According to the data obtained, phylogenetic trees based on the ITS region were found to be more useful than phylogenetic trees based on the trnL-F region. Estimates of genetic distance showed that the Hue Ochna samples were genetically homogeneous and were not correlated with geographic distance according to a Mantel test (r = 0.1842). This study is the first report on constructing a molecular database of Hue Ochna in Vietnam. Our findings have provided useful information for further identifying the genetic plant sources for propagation, development, and conservation of the highvalued economic materials of Hue Ochna