Abstract: Premise of the study: Microsatellite primers were developed for Carex helodes, a western Mediterranean endemic locally distributed in southern Portugal and southwestern Spain, and rare in northern Morocco. Methods and Results: 109 nuclear microsatellite markers were developed using a shotgun pyrosequencing method, resulting in 91 polymorphic and 18 monomorphic loci when tested using 19 individuals sampled from 5 populations from Portugal, Spain and Morocco. Loci averaged 3.23 alleles per locus (SD = 1.15). In a single population (Cortelha population, Portugal), the 34 most polymorphic loci showed a mean observed heterozygosity of 0.357 (SD = 0.292) and expected heterozygosity mean of 0.384 (SD = 0.255). Conclusions: Next generation sequencing allows us to develop a high number of genetic markers whose levels of polymorphism are adequate to study gene flow among populations. However, when genotyping the individuals within a population, we found low levels of variation. Juan Miguel Arroyo, Marcial Escudero & pedro jordano. 2016. Isolation of 91 polymorphic loci in the western Mediterranean endemic Carex helodes (Cyperaceae). Applications in Plant Sciences, 4, 1500085. LINK.