Hybrids between cultivated and wild sunflowers (Helianthus annuus) are frequently reported. As much as 42% of progeny from wild plants near cultivar fields are hybrids, and cultivar genes have been shown to persist in wild populations at least five generations. We report the effects of up to 40 years of persistent cultivar gene flow on the genetic structure of three wild H. annuus populations that are adjacent to cultivated fields. Eighteen cultivar-specific markers were surveyed in a total of 115 individuals. We also developed cultivar-based genetic maps for the markers and used them to see if marker patterns in the wild populations were consistent with introgression and if selection was acting jointly on unlinked loci. High levels of crop specific markers were detected in all three wild populations, ranging from 0.315 to 0.382, on average. All 115 plants had at least 1 cultivar marker. Introgression is the most likely explanation for the presence of crop specific markers in the sympatric populations because (1) the markers were either not present or found at much lower levels in four allopatric populations, (2) markers that were genetically linked in the cultivar invariably showed linkage disequilibrium patterns in the sympatric populations consistent with introgression, and (3) homology tests ruled out convergent evolution as an alternate explanation. Hence, introgression of cultivar loci was widespread, and the sympatric wild populations have been replaced by advanced generation hybrids. Unlinked, introgressed markers did not show significant linkage disequilibria, indicating a lack of epistatic associations among introgressed markers. Hence, transgenes in cultivated sunflowers should readily introgress into sympatric wild populations, and their fate will be determined primarily by their fitness effects on the wild plants.