The levels and pattern of the genetic variation within and among populations of the endangered fern Ceratopteris pteridoides (Hook.) Hieron in China were investigated using inter-simple sequence repeat (ISSR) markers. Thirteen ISSR primers used in the study amplified 125 reproducible bands with 56 (PPB=44.8%) being polymorphic, indicating a relative low level of genetic diversity at the species level. Genetic diversity varied greatly among populations with the PPB values ranging from 14.4% to 32%. The coefficient of genetic differentiation between populations (G st ) was 0.297, indicating low level of genetic variation between C. pteridoides populations. AMOVA analysis also revealed a low level of genetic differentiation among the five populations. Of the total genetic diversity, 26.17% was attributable to among-population diversity. The UPGMA cluster of all samples showed that individuals from the same population occasionally failed to cluster in one distinct group indicating extensive inter-population gene flow among the remaining populations of C. pteridoides in China. A Mantel test showed no significant correlation between genetic distance and geographic distance (r=0.44, P=0.91) suggesting that gene flow was not restricted geographically. A number of ways including clonal growth, genetic drift and inbreeding, the extensive hydrologic connectivity among populations, which facilitated long-distance gene flow, might have affected the genetic profiles of C. pteridoides.