Suppression of invasive Canada thistle, Cirsium arvense, with biological control agents has stalled because introduced agents were not host-specific. To aid in the development of more effective management strategies, molecular markers are needed to examine the genetic structure of Canada thistle populations. Microsatellite (simple sequence repeat) markers were developed and intersimple sequence repeat (ISSR) markers were tested for North American populations. An average of nine polymorphic alleles per microsatellite locus and 11 per ISSR locus were detected. These will be used to examine the genetic structure of C. arvense in the northern Great Plains and their transferability to endemic Cirsium spp.