Swertia perennis s. l. ranges discontinuously across Eurasia to the mountains of western North America in a series of geographic isolates sometimes recognized as distinct taxa. We sequenced the chloroplast trnL intron, the trnL-trnF intergenic spacer, and the trnH-psbA spacer from 26 North American populations of S. perennis, two Altai populations, and ten outgroup taxa, and analyzed these data with previously published sequences. Combined data from trnL, trnL-trnF, and trnH-psbA yielded 11 distinct haplotypes from North America and two from the Altai. Phylogenetic analyses resolve rooted phylogenies of chloroplast lineages within North American S. perennis. In our sample, some lineages have well-characterized, non-overlapping geographic ranges. Further sampling will likely reveal additional haplotypes and polymorphism within populations or geographic areas, but this study lays a foundation for investigations of phylogenetic biogeography in S. perennis and co-distributed species.