Abstract: Taxus chinensis var. mairei, one of the tertiary relic species, is one of the state first class protected species and endemic to China. Over the course of three years, we observed the external morphological changes from cone bud emergence to seed cone formation and the internal cellular changes during megasporogenesis, gametophyte development and embryo-genesis using paraffin-embedded-sectioning and hematoxylin-staining methods. Most ovules were only orthotropous, but two ovules wrapped within one bract could be seen occasionally. The meiotic division of the megasporocyte produced four megaspores in a linear tetrad formation. The three megaspores near the micropyle disintegrated, while the largest spore near the chalaza developed into a functional megaspore. 256 free nuclei were produced by a series of mitoses of the functional megaspore. The number of the archegonia varied from 2 to 6, and were not grouped together. There was about two months from pollination to fertilization. The pro-embryo was standard. Wall formation was initiated at the stake of about 16 free nuclei in the pro-embryo. Simple and cleaved polyembryony were found frequently, and the development of the embryo was not synchronous. The above characteristic structures of female gametophyte development, including the orthotropous ovule, number of free nuclei, the interval between pollination and fertilization, and the number of pro-embryo free nuclei, were fundamentally similar to Cupressaceae (s.l.), but different from Pinnace. Therefore we support that Taxaceae be under Cupressaceae (s.l.). We found no abnormal phenomena in the megasporogenesis and development of female gametophytes, and thus this is not the cause of this species endangerment.