<p>Numerous studies have examined the reproductive systems of threatened orchids to develop effective conservation strategies. However, the detrimental effects of seed predators on seed production are often overlooked. In this study, we evaluated the impact of the seed-parasitic fly <i>Japanagromyza tokunagai</i> on the seed production of the endangered orchid <i>Cephalanthera falcata</i>, based on observations from five locations over one year and from a single location over four years in Chiba Prefecture, Japan. Our findings showed that <i>J. tokunagai</i> caused 100% capsule damage across all sites and years examined. Although some infested fruits still produced seeds in certain locations and years, the quantities were very low. Consequently, we observed a 99.1–100% reduction in seed production across all populations investigated. These results suggest that reduced seed production could limit generational turnover, potentially threatening the reproductive success and long-term survival of <i>C. falcata</i>, at least in the populations studied. This highlights the need to mitigate the negative impact of <i>J. tokunagai</i> on seed production in <i>C. falcata</i>. Combining artificial pollination with the bagging of individual inflorescences could be an effective approach, capable of increasing seed production by more than 100-fold. Given the fungal dependence and low germination rates of <i>C. falcata</i>, future work should also examine seedling recruitment to better understand the impacts of seed loss and improve estimates of long-term resilience.</p>