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Plant functional connectivity integrates species-environment interactions, dispersal vectors, and landscape structure variables to understand species’ spatial responses to habitat fragmentation. Functional connectivity is still poorly understood for aquatic plants despite the promise it holds for informing wetland conservation across landscapes. Through a landscape genetics approach, we quantified plant functional connectivity among geographically isolated wetlands by genotyping seven nuclear microsatellite loci in 18 populations of Nymphoides fallax, a tetraploid aquatic plant endemic to Mexican and Guatemalan highland wetlands. We tested if wetland connectivity, quantified with three connectivity indices, translated to high genetic diversity within populations and if geographical distance per se explained gene flow among wetlands. We also tested if landscape features such as vegetation and surface water cover …