Knowing the origin of invasive taxa, whether multiple introductions have occurred, and levels of genetic variation relative to the native range, is vital to conducting rigorous tests of hypotheses to explain biological invasions. We explore phylogeographical relationships of two Eurasian knapweed taxa that are invasive in North America, Centaurea diffusa and C. stoebe micranthos (Asteraceae), using chloroplast DNA intron sequences. We also gathered data from C. stoebe stoebe, hybrids between C. diffusa and C. stoebe stoebe (C. xpsammogena), and three other species in the genus. We sequenced 213 individuals from Eurasia and North America, and found 22 haplotypes. Centaurea diffusa has lower haplotype diversity and allelic richness in the introduced range relative to the native range. Even with reduced variation, the data suggest at least two introductions of C. diffusa. There is a trend towards reduced variation in C. stoebe micranthos, but it is not significant. One of the haplotypes found in North American C. stoebe micranthos matches a haplotype from a taxon other than C. stoebe micranthos in Europe. This suggests introgression of the chloroplast between taxa, or possibly the invasion of another Centaurea taxon into North America. Additionally, C. diffusa, C. stoebe micranthos, and C. stoebe stoebe share several haplotypes, including their most common haplotype. This suggests ongoing hybridization between the species or incomplete segregation. These data can guide further exploration for the origins of these species, and point out locations within the introduced range with unique and diverse genetic makeup.