To understand genetic variability of the endangered aquatic herb Brasenia schreberi (Cabombaceae), we describe 31 microsatellite markers obtained using next-generation sequencing. A total of 24 individuals from the population of Jackson Lake, USA, were genotyped for each marker. Twenty-eight markers were polymorphic. The number of alleles per locus ranged from 1 to 9; the observed and expected heterozygosities ranged from 0 to 1 and from 0 to 0.751, respectively. These markers should be useful tools for genetic variation and conservation studies of B. schreberi.