Genetic markers have been used in horticulture and conservation biology to identify breeding lines, assess genetic diversity, and examine gene flow. In weed science, analysis of genetic markers is not as common, as the focus often lies in the development of control methods. This is unfortunate, because advances in genetic marker techniques may lead to innovative methods in controlling weedy plants. Microsatellites, random amplified polymorphic DNA (RAPDs), intersimple sequence repeats (ISSRs), amplified fragment length polymorphisms (AFLPs), DNA sequences, single nucleotide polymorphisms (SNPs), and derived cleaved amplified polymorphic sequences (dCAPS) have been used in studying genetics of weedy plants. Beyond assessing genetic diversity of weeds, markers have been used to examine gene flow, patterns of dispersal, ploidy levels, and relationships of weedy and nonweedy species, as well as identifying founder populations. Identification of closely related species may indicate the potential for hybridization, cross reactivity of chemical applications, or nontarget biological control effects. Furthermore, markers have been used in identification of mutations conferring herbicide resistance and identification of regions correlating fitness of weedy and hybrid plants in new habitats. Knowledge from genetic markers provides fundamental information that can be used in advancing chemical and biological control in weed management. This article serves as a review of these marker types and their application to weed science.