Wetlands are natural links between terrestrial and aquatic ecosystems maintaining biodiversity at regional and landscape levels. Wetland conservation in Mexico could benefit from understanding functional connectivity for aquatic plants. This is an ongoing research project aimed at identifying the landscape factors that determine gene flow and genetic diversity of Schoenoplectus californicus in the highland wetlands of Central-Western Mexico. Between 10 to 30 leaf tissue samples from S. californicus individuals were collected in natural and artificial wetlands in the states of Michoacán, Guanajuato, and Jalisco for genomic DNA extraction. A total of sixteen nuclear microsatellite markers developed for S. americanus will be transferred and genotyped to estimate genetic diversity and differentiation and to statistically test their relationship with landscape elements. To date, 419 individuals from 27 sites have been sampled from 11 wetlands. Six out of 16 microsatellites have been transferred. The results of this work will guide the design of wetland management and conservation strategies at the landscape scale, particularly in anthropogenic landscapes where wetlands are at high risk.