Millions of square kilometers of the Earth’s surface is covered by forest fragments, and a quarter of remaining tropical forest has been fragmented. In Southeast Asia, about 650,000 ha of natural forests are fragmented per year. Fragmentation of old growth forests is considered to be the greatest threat to tropical forest biodiversity. Forest fragmentation has many negative effects on tree species. It causes edge effects, reduces population sizes and increases isolation between populations. This has potentially large implications for tree species and forest dynamics. In this study, the effects of forest fragmentation on tree diversity, population dynamics, and genetic diversity in Vietnam are analyzed. Our results suggested that small forest fragments (1-10 ha) still retain a significant amount tree species richness, and that large forest fragments (≥ 100 ha) are similar to continuous forest in terms of forest structure, species richness and species composition. And small fragment size limits the viability of our study species, but that these species have rather good prospects to survive in fragments of >20 ha. In addition, strong spatial genetic structure and a relatively low genetic diversity in adults in forest fragments, suggesting a genetic bottleneck due to the decline of the original population. Allele richness was lower in seedlings compared to adults, showing that populations continued to lose genetic variation after the fragmentation event. In contrast, observed and expected heterozygosity were generally not reduced in seedlings. This may indicate that a new genetic equilibrium has not been reached yet in remnant populations , but may also be caused by the observed high levels of pollen and seed influx in fragments. In summary, forest fragmentation has many negative effects on the remaining tree population. Recommendations for forest fragmentation research in Vietnam are proposed.