In this study, the mating system of the endangered aquatic fern Ceratopteris thalictroides in China was investigated using microsatellite markers. The estimates of the multilocus outcrossing rate (tm) and single-locus outcrossing rate (ts) were high at the species level (tm = 0.701 and ts = 0.595, respectively), indicating that C. thalictroides is a predominantly outcrossing species. Negative F (inbreeding coefficient of the maternal parents) values (-0.137) at the species level indicated an excess of heterozygotes and low inbreeding in the populations analyzed. Our investigation revealed that some of the natural and ex situ conservation populations of C. thalictroides have a prolific capacity for vegetative growth. The results showed that the homosporous pteridophyte C. thalictroides in China predominantly favors gametophytic crossing with a certain level of inbreeding along with vegetative growth. Ten populations have been established for ex situ conservation in Wuhan, China, with a survival rate of more than 90%, and mature spores were collected from them. Several factors, including high dispersal of spores and gametophytes by flowing water, high gene flow, and the wide distribution of the species in China, with the occurrence of some large populations, may have resulted in a high outcrossing rate in Chinese C. thalictroides. The high outcrossing rate of C. thalictroides showed that ex situ plantings are most suitable for enhancing possible mixing of the different populations, thus minimizing inbreeding.