Dispersal is a key evolutionary force affecting gene flow and genetic diversity. Therefore, analysis of population

connectivity plays an important role in protecting endangered species. Ottelia acuminata var. jingxiensis is a perennial endangered aquatic plant, and present in several karst rivers of Yunnan–Guizhou Plateau. We estimated the genetic variation and population connectivity by nuclear microsatellites in 11 populations mainly from three rivers. The plant showed low genetic diversity (HE=0.205–0.367), which was mainly explained by its critically restricted geographical range. Meanwhile, relatively low genetic differentiation (FST = 0.186; G”ST = 0.242) was found compared with that of other studies about varieties of O. acuminata in isolated habitats. Cluster analyses based on different approaches consistently showed populations from the same river clustered together, suggesting water flow acting as corridors for dispersal; additionally, bidirectional gene flows within and among rivers indicated that zoochory or mankind were also major contributors to gene exchange. The results showed that contemporary gene flow was much lower than historical gene flow, suggesting that recent habitat fragmentation resulted in decreased gene flow. We recommend watercourse dredging within rivers to enhance habitat stability and to improve connectivity among populations. In addition, the different populations from different rivers or isolated habitats should be protected to maintain the genetic diversity.