• Premise of the study: Microsatellite markers were developed for the common wetland plant Juncus effusus to assess levels of within- and among-population genetic diversity.

• Methods and Results: Using a next-generation sequencing approach we identified new microsatellite loci, from which 23 were further characterized in a large population of J. effusus. Expected heterozygosity ranged from 0 to 0.64 with a mean of 0.407. Inbreeding coefficients (mean = 0.984) were very high, confirming earlier suggestions of an inbred mating system. Cross-amplification was tested in J. conglomeratus, J. inflexus, J. drummondii, and J. filiformis, with best results in the former.

• Conclusions: The described microsatellite markers will be helpful in assisting studies on, e.g., reproduction, taxonomy, and phylogeography in J. effusus and related species.