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Accurate identification of Arctic plant species is critical for understanding potential climate-induced changes in their diversity and distributions. To facilitate rapid identification we generated DNA barcodes for the core plastid barcode loci ( rbcL  and  matK ) for 490 vascular plant species, representing nearly half of the Canadian Arctic flora and 93% of the flora of the Canadian Arctic Archipelago. Sequence recovery was higher for  rbcL  than  matK  (93% and 81%), and  rbcL  was easier to recover than  matK  from herbarium specimens (92% and 77%). Distance-based and sequence-similarity analyses of combined  rbcL  +  matK  data discriminate 97% of genera, 56% of species, and 7% of infraspecific taxa. There is a significant negative correlation between the number of species sampled per genus and the percent species resolution per genus. We characterize barcode variation in detail in the ten largest genera sampled ( Carex ,  Draba ,  Festuca ,  Pedicularis ,  Poa ,  Potentilla ,  Puccinellia ,  Ranunculus, Salix , and  Saxifraga ) in the context of their phylogenetic relationships and taxonomy. Discrimination with the core barcode loci in these genera ranges from 0% in  Salix  to 85% in  Carex . Haplotype variation in multiple genera does not correspond to species boundaries, including  Taraxacum , in which the distribution of plastid haplotypes among Arctic species is consistent with plastid variation documented in non-Arctic species. Introgression of  Poa glauca  plastid DNA into multiple individuals of  P. hartzii  is problematic for identification of these species with DNA barcodes. Of three supplementary barcode loci ( psbA–trnH ,  psbK–psbI ,  atpF–atpH ) collected for a subset of  Poa  and  Puccinellia  species, only  atpF–atpH  improved discrimination in  Puccinellia , compared with  rbcL  and  matK . Variation in  matK  in  Vaccinium uliginosum  and  rbcL  in  Saxifraga oppositifolia  corresponds to variation in other loci used to characterize the phylogeographic histories of these Arctic-alpine species.

DNA Barcoding the Canadian Arctic Flora: Core Plastid Barcodes (rbcL + matK) for 490 Vascular Plant Species