Nypa fruticans Wurmb is both a relic plant and a true mangrove. In China, wild populations are distributed only on Hainan Island and face significant challenges in regeneration from seedlings. This study explored the underlying causes of recruitment limitation by examining seed morphological traits from three distinct populations (Haikou, Wenchang and Wanning) and analysing seed germination and seedling growth characteristics under varying conditions. The key findings are as follows: fruiting and seed-setting rates for N. fruticans were notably low, standing at only 21 and 40%, respectively. The Wanning population exhibited significantly higher rates compared to the other two populations. Under natural conditions, the germination and seedling emergence rates were also modest, at 36.58 and 22.99%, respectively. The germination and emergence rates of the Wanning population were significantly greater than those of the Haikou and Wenchang populations. Meanwhile, seeds from a single population did not differ in germination rates among three in situ N. fruticans habitats, but seedling emergence rates differed significantly. Optimal conditions for seed germination involved a light intensity of 60%, a salinity of 5‰ and a flooding time of 8 h/day. In natural settings, these three environmental factors fall short of the ideal conditions. The study underscores that light, salinity and flooding are primary factors contributing to the limitations in N. fruticans seedling recruitment. In addition to advocating increased investment in scientific research and technology to address seed source issues, we recommend heightened efforts in habitat restoration, in situ conservation and the optimization of relocation and field return strategies to bolster N. fruticans populations.