Mitochondrial gene barcoding is a useful way of identifying unknown specimens; however, their effectiveness in distinguishing between anthozoans remains controversial. It has been demonstrated that anthazoans have unusually slow evolving mitochondrial genomes and therefore lack sufficient variation for differentiation at low taxonomic levels. However, DNA barcodes have proven useful for analysis of scleratinian corals, and studies on the less well known octocorals, a sub-class of anthozoa, have shown some improvements in taxonomic identification with the use of more gene sequences to gain greater phylogenetic resolution. Here we present work on the phylogenetic analysis of octocorals collected throughout the NW Atlantic using three mitochondrial gene barcodes to test the ability of this combination to distinguish between known octocoral species. Octocoral specimens were collected from the Bay of Biscay and waters surrounding the Azores, Ireland, NW Scotland, and Iceland. Total DNA was extracted from samples and each sequenced for three mitochondrial regions: the ND2 subunit of NADH dehydrogenase, the “Folmer region” of COI with an adjacent intergenic region igr1, and the octocoral specific mitochondrial protein coding gene msh1. Phylogenetic reconstruction was performed on 144 samples by combining all three barcode regions and results were compared with morphological identifications of the specimens.