The German tamarisk (Myricaria germanica) is a riparian shrub threatened in Europe, where populations are largely confined to the upstream areas of rivers. To study gene movement in this species within and among catchments, we isolated and characterized 22 nuclear and 5 chloroplast microsatellite loci and tested their polymorphism based on 40 individuals of M. germanica and four individuals of Myricaria rosea. For M. rosea, 15 markers amplified, and of these, eight were polymorphic. All markers were polymorphic for M. germanica. The polymorphic markers allow the characterization of gene flow patterns at various spatio-temporal scales.