Spotted knapweed (Centaurea stoebe) and brown knapweed (Centaurea jacea) are members of the Asteraceae and natives of Eurasia. Centaurea stoebe is a major invasive species in North America, dominating large stretches of grassland. It also is known to form hybrids in North America with closely related naturalized Centaurea spp., including C. jacea. Both species were introduced on Nantucket Island, a coastal island 44 km south of Cape Cod, Massachusetts, and morphologically unusual, possible hybrid populations have been reported. The aim of this study was to test for hybridization between these weeds in an isolated setting. Chloroplast marker sequences revealed that all the hybrid-like plants shared the same haplotype with C. jacea populations. The analysis of nuclear markers with microsatellite markers showed surprisingly little intra- and inter-specific gene flow between populations and no evidence of hybridization between C. stoebe and C. jacea. Two populations with hybrid-like morphology are most likely environmental plastic morphs of C. jacea.