This investigation documents the key anatomical features in embryo development of Cypripedium formosanum Hayata, in association with the ability of embryos to germinate in vitro, and examines the effects of culture media and seed pretreatments on seed germination. A better understanding of zygotic embryogenesis for the Cypripedium L. species would provide insights into subsequent germination events and aid in the in vitro propagation of these endangered species. In seeds collected at 60 days after pollination (DAP), soon after fertilization, no germination was recorded. The best overall germination was found at 90 DAP (≈70%), at which time early globular to globular embryos with a single-celled suspensors can be observed. After 135 DAP, the seeds germinated poorly. At this time the inner integument shrinks and forms a tight layer, which encloses the embryo, the so-called “carapace.” Using Nile red stain, a cuticular substance was detected in the carapace, which may play a role in the impermeability of the mature seed and may help the seeds survive in the stringent environment. At maturity (after 210 DAP), the embryo proper has an average size of eight cells along its length and six cells across the width. Lipids and proteins are the main storage products within the embryo. To improve seed germination, experiments were conducted to test the suitability of various media and pretreatments of seeds. When different media were used, except for the Harvais medium at 120 DAP, there was no significant difference in seed germination at three different developmental stages tested. Soaking mature seeds in 1% NaOCl or treating them with ultrasound may slightly increase the germination percentage. For seed germination, our results indicate that the timing of seed collection outweighs the composition of medium and the seed pretreatments.