Abstract: Manglietia patungensis, an endangered tree species endemic to China, is listed in National Key Protected Species. To explore the underlying mechanisms relevant to the impediment in its sexual reproduction, we studied the morphological and physiological characteristics of seeds during its dormancy and after-ripening process. The results showed that the incomplete development of embryos was the main reason for seed dormancy. The immature embryos continued differentiating and developing during the after-ripening process. As the seed coat was permeable, it would not induce seed dormancy. Germination inhibitors existed in different parts of seeds, especially in the endosperm, which was believed to be a major factor for the ger-mination delay. Endogenous hormone ABA and IAA played an important role in the dormancy and germina-tion of seeds. ABA was the key factor for seeds dormancy while IAA benefited germination. Therefore, the change of IAA/ABA ratio was crucial to seed dormancy and germination. Only at a temperature as low as 4°C and in a humid environment, could M. patungensis seeds complete the morphological and physiological after-ripening process. In fact, it was observed that the after-ripening process of M. patungensis seeds oc-curred in autumn, a season characterized by low rainfall and drought in this area. Evidently, viability loss of seeds caused by water deficit during the after-ripening period may explain the poor regeneration of this spe-cies.