Wild rice (Zizania palustris) is a North American, aquatic grass. It occurs in Minnesota, Wisconsin, Michigan and into Canada and can be found in shallow lakes and slow-moving rivers. Wild rice grain is harvested for food and is culturally important to Ojibwe Native Americans. The plant is an out-crossing species and when inbred, the offspring suffer severe inbreeding depression. Several cultivated varieties have been produced by the breeding program at the University of Minnesota over the past forty years, but the species is not yet fully domesticated. While the naturally-occurring, native wild rice populations have served as a source of germplasm for the breeding program, little is known about the genetic diversity within and among them. Cultivated varieties are developed using the phenotypic recurrent selection breeding method with a relatively high selection pressure for several agronomic traits. A set of polymorphic SSR markers was used to measure genetic diversity among and within twenty-one natural wild rice populations from Minnesota and Wisconsin and six cultivated wild rice populations from the University of Minnesota breeding program. The results indicated that natural wild rice populations are genetically diverse from one another while the genetic diversity of the breeding program germplasm is relatively narrow.