Sweet cherries (Prunus avium) have become one of the most competitive Chilean export fruit crops. The cherry fruit industry has the potential to expand and increase the production, quality and volume of exported cherries. Towards this end, a marker-assisted cherry breeding program has been established between investigators at Universidad Católica de Valparaíso and Universidad Andrés Bello (www.biocerezas.cl). To begin this breeding program, cultivars in Chile as well as cultivars to be imported must be differentiated molecularly. We have identified eight SSR molecular markers that may be used to genotype 13 sweet cherry varieties to be used in the breeding program.