Abstract:I.yunguiensis is one of the existing ancient relict plant only distributed in Yunnan-Guizhou Plateau, which is a important sample to the study on paleoecology and plant evolutionary in Yunnan and Guizhou area, because of the sharp attenuation of its wildlife groups, I. yunguiensis was listed as the first grade state protection, but so far, we do not yet know its endangered mechanism clearly. In this study, the I. yunguiensis female gametophyte come from artificial culture, we use semithin section technology to observe every development phase of it, and the results are as follows: 1.The germination rate of megaspore is 26%; 2.The female gametophyte is heterotrophic, and development in the megaspore membrane during its lifetime; 3.There are only two neck canal cells and zero ventral canal cell in the female gametophyte of I. yunguiensis. 4.Reported the relevance between the egg and the neck canal cell, useing parafin section; 5.The mainly barriers of the female reproductive structure contains the following points, female gametophyte stop developing during the free nuclear stage, less neck wall cell or arranged disorders, neck canal cell abnormal, the apoptosis of egg and so on. This article provided informative gist both in reproductive biology and endangered mechanism study, the free nuclear is one of important steps in reproductive biology and systematics study of Isoetes; The missing ventral canal cell may be a characteristic of the simplified evolutions about Isoetes.