Abstract: Habitat fragmentation is one of the most serious threats to plant diversity. In general, fragmentation negatively impacts the genetic variability of plant populations due to increased random genetic drift, inbreeding, and reductions in gene flow. To investigate the effect of habitat fragmentation on genetic diversity and the mating system of Tsoongiodendron odorum, in this study, we analyzed genetic diversity and the mating system in hierarchical levels at the population, stands, and the individual scales in a fragmented T. odorum population. We sampled and mapped 61 adult individuals from the population. Using eight microsatellite loci, we genotyped a total of 780 seeds from 15 maternal trees for the mating system analysis. The results revealed moderate levels of genetic diversity in both adults (H_E = 0.522) and seeds (H_E = 0.499) with no significant differences between the two ontogenic stages. In addition, we did not observe a significant increase in the seeds inbreeding coefficient. Results from the multilocus mating system analysis indicated that T. odorum was an outbreeding species with a multilocus outcrossing rate (t_m) of 1.000. A small number of biparental inbreeding and correlated mating events were detected in this fragmented population. We found a small number of effective pollen donors (N_ep is between 3.7 and 5.4), which seems to be a common character of insect-pollinated canopy trees. Minor differences in outcrossing rates were detected among stands, and more pollen donors were found in smaller stands. However, outcrossing rate was significantly different among individuals, and a few selfing events were detected in some seed trees. These results may provide fundamental information required to establish long term conservation strategies for this endangered tree which is endemic to China.