Sei whale (Balaenoptera borealis) is a very rare species in the North Sea. The remains of four whales identified as sei whales, originating from the Netherlands, are preserved in the zoological collection of Naturalis Biodiversity Center, Leiden, the Netherlands. A single bone in the Naturalis collection, found on the Dogger Bank just outside Dutch waters, was also identified as sei whale. Because there were doubts about identification of several specimens, three of them were genotyped, using partial 16S, COI, ND4L, CytB and D-loop sequences, which are standard DNA barcoding markers. The holotype of Sibbaldius schlegelii (Flower, 1864) [= B. b. schlegelii] from Pekalongan, Indonesia, and a fin whale (B. physalus) from the Netherlands were included for comparison. Three of the six specimens turned out to be incorrectly identified. The results underscore the added value of molecular identification of skeletons, and of museum collections. On the basis of our results, we cannot distinguish between the southern hemisphere subspecies of sei whale, B. b. schlegelii and B. b. borealis.