In this paper, the base of nation level protected species Isoetes orientalis is used as materials. With the method of slice technology, we anatomically observed the development process of female gametophytes and embryos, and discussed the reproduction and endangered mechanism. The results showed that: (1) Megaspore of I. orientalis would be germinated within 3-5 d, the mature gametophytes were emerging spherical and forming a number of archegonias with triplets but no rhizoids. There were neck cells and neck canal cells in the archegonium, but no ventral canal cells. (2) Most of the female gametophytes were only developed into one embryo, occasionally into more embryos. During the development of embryo, the first primordium growth rapidly than the second and third primordiums. (3) The part tissue of archegonium often appear differentiation disorder and lead to female gametophyte abortion. The results supported the Phyllorhize Theory, also discussed the ventral canal cells degenerated and two embryos mechanism. We speculated that the gametophyte in I. orientalis usually stopped during free nuclei stage, morphology and anomaly site of archegonia and eggs arranged in disorder might be the causes of abortion.