Rapid and recent lineage radiations pose challenges to systematists. Using members of the highly diverse Simulium arcticum Malloch complex, we tested whether the cytochrome c oxidase subunit I (COI) barcoding gene can differentiate black fly sibling species. Members of the S. arcticum complex were monophyletic in relation to two morphospecies and two cryptic species of the Simulium malyschevi Dorogostaisky et al. and Simulium noelleri Friederichs species-groups, respectively. Of five S. arcticum sibling species analysed, only Simulium negativum Adler et al. was monophyletic. No other members of the complex could be distinguished using COI barcodes. The inability to resolve S. arcticum sibling species resulted because (1) haplotypes were shared between species and (2) the distribution of interspecific genetic distances completely overlapped the range of variation within species. Potential sources of incongruence between barcode data and species boundaries include imperfect taxonomy, inadequate genetic information, incomplete lineage sorting, and/or introgressive hybridization. We ruled out imperfect taxonomy because chromosomal, ecological, and distributional evidence support the validity of S. arcticum sibling species. Therefore, current nomenclature should be maintained pending further study. We conclude that one or more of the latter three sources of incongruence could be responsible for the lack of reciprocal monophyly among species of the S. arcticum complex.