Ancient trees remaining in natural areas from once widespread forest due to overexploitation and habitat modification would naturally regenerate to form small isolated populations after the halting of disturbance. The genetic processes and consequence of this regeneration are generally unknown, which prevents the effective conservation and management of these populations. One such population, an Erythrophleum fordii population, is located in Dinghushan National Nature Reserve (China). Owing to the remarkably huge trunk of the sole ancient tree (KG) relative to the other individuals in the population, the local people and local tourism administration presume that this population has developed solely from KG. We found, using genetic diversity analyses, that contrary to this presumption, the population might have regenerated from several founders with diverse genetic backgrounds. Severe degradation of genetic diversity within the population did not take place, rather, it possessed the potential ability to maintain and recover gradually with population development. According to the results of simulations, we found that the longevity of tree species with iteroparity offers the potential to maintain genetic diversity in small isolated populations. The results from this study will benefit the restoration and conservation of the endangered species E. fordii, and of other congener species and tree species with similar life history traits.