Tropical forests, a key category of land ecosystems, are faced with the world’s highest levels of habitat conversion and associated biodiversity loss. In tropical Asia, Dipterocarpaceae is one of the economically and ecologically most important tree families, but their genomic diversity and evolution remain understudied, hampered by a lack of available genetic resources. Southern China represents the northern limit for Dipterocarpaceae and thus changes in habitat ecology, community composition, and adaptability to climatic conditions are of particular interest in this group. Phylogenomics is a tool for exploring both biodiversity and evolutionary relationships through space and time using plastome, nuclear and mitochondrial genomes. We generated full plastome and Nuclear Ribosomal Cistron (NRC) data for Chinese Dipterocarpaceae species as a first step to improve our understanding of their ecology and evolutionary relationships. We generated the plastome of Dipterocarpus turbinates, the species with the widest distribution using it as a baseline for comparisons with other taxa. Results showed a low level of genomic diversity among analyzed range-edge species, and different evolutionary histories of the incongruent NRC and plastome data. Genomic resources provided in this study will serve as a starting point for future studies on conservation and sustainable use of these dominant forest taxa, phylogenomics, and evolutionary studies.