Ceratopteris thalictroides is a semi-aquatic fern with a circumtropical distribution. Because this species is designated internationally on the IUCN Red List as requiring at least some concern, Korean popu- lations are of great concern for the species’ long-term survival, as they are at the northern limit of the species distribution. To establish an effective conservation strategy for those populations at the genetic level, we used the Mi-Seq platform to develop three sets of 25 polymorphic microsatellite markers for C. thalictroides, which is endangered in Korea. In populations sampled from Busan and Gochang, the number of alleles ranged from 2 to 13 (average of 5.64), and plants presented an expected heterozygosity of 0.000 to 0.860. These markers will be useful for evaluating the genetic status and conserving Korean populations of C. thalictroides more effectively.