Heart-podded hoary cress, Lepidium draba L. ssp. draba (Brassicaceae) is a noxious invasive weed in the USA. At present, efficient biological control of this Eurasian native weed in the USA is hampered by lack of knowledge of its population genetic structure and colonization process. Here, we describe the development of 11 polymorphic microsatellite markers that also reveal the polyploidy of this weed. Successful cross-species amplification highlights the possibility of using these markers for genetic studies in other closely related species.