Abstract Aim To describe current geographical patterns of genetic diversity and infer the historical population dynamics of the stone oaks (Lithocarpus) in Southeast Asia. Location We sampled three populations in Indochina: (1) Yunnan province, China; (2) Pyin Oo Lwin area, Myanmar and (3) north-western Vietnam; two in western Borneo: (1) South-western Sarawak and (2) West Kalimantan, Indonesia; two in central Borneo: (1) north coastal Sarawak and (2) north-eastern Sarawak, Malaysia; and two in northern Borneo: (1) Central Sabah and (2) Northern Sabah, Malaysia. Methods A phylogenetic reconstruction of chloroplast DNA sequence variation from numerous individuals of multiple species was used to determine geographical distribution of genetic diversity. A resampling scheme was used to determine the significance of these patterns at different hierarchical levels of the phylogeny. Results were compared with a previously published set of nuclear DNA sequence data. Results A high level of chloroplast sequence variation was found, which was divided equally between two major clades separated by four non-homoplasious changes. One clade was confined to the island of Borneo, while the other was widespread. Strong geographical structure was observed in the chloroplast sequence variation. The Indo-chinese populations were much more closely related than expected, comparable with the highly endemic and isolated population on the western coast of Borneo. Conversely, individuals from the Kelabit Highlands were found to be more distantly related than expected. The highest levels of genetic endemism were observed in western Borneo. More geographical structure was observed in the Bornean clade than in the Widespread clade, because of limited genetic diversity in the Widespread clade. Relatively weak geographical structure was found in the nuclear sequence variation: only populations in southern China and central Sabah were significantly related. Conclusions The high levels of chloroplast genetic diversity and the persistence of an ancestral haplotype that is a single step away from a haplotype found in Castanopsis indicates the continuous presence of tropical rain forest in Southeast Asia throughout the evolutionary history of the genus (c. 40 Myr). This conclusion is supported by the high frequency of numerous endemic types observed in every population and the relatively few number of ‘missing’ haplotypes. This situation suggests both limited migration and limited extinction. In contrast, the nuclear genetic diversity contained less geographical structure, indicating that our taxonomic sampling among populations was unbiased and that gene flow mediated through pollen is less geographically restricted and contains less geographical structure than purely seed-mediated (chloroplast) gene flow. The most likely scenario suggested by the evidence involves four major patterns: (1) the widespread presence of an ancestral haplotype; (2) the large degree of separation (four non-homoplasious base pairs) between the types found in the two major clades; (3) the concentration of derived types from both major clades found in central and northern Borneo; and (4) the molecular endemism found in each location. These patterns suggest four primary things about the population dynamics of Lithocarpus since the late Eocene: (1) populations have either spanned the entire region throughout much of the evolutionary history of the genus or substantial populations have persisted in both Indochina and Borneo with limited migration between them; (2) significant fragmentation has occurred subsequently between the Asian mainland and the Melasian island archipelago, leading to independent genetic diversification in both regions; (3) several locations possessing significant independent histories, have experienced little migration and have never gone completely extinct; and (4) that the central highlands of Borneo have been re-invaded from the north and the west. The timing of these events is difficult to ascertain but probably predate the Quaternary Period, suggesting that although the recent ice ages might have affected the overall distribution of rain forest in Southeast Asia, it managed to persist in most regions even through the most dramatic drying events.