The control region (CR) of the mitochondrial DNA has been previously used to decipher the population structure of Holocene bowhead whales (Balaena mysticetus) from the Spitsbergen stock. The bone samples dated from recent to more than 50000 years BP were collected on the elevated beaches of Svalbard, and are related to ancestors of the nearly extinct Spitsbergen stock. Very high haplotype diversity was reported that frequency based analyses and comparisons with other data set became meaningless; More than 80 % of the specimens had individual specific haplotypes. Therefore, it was of large interest to investigate the genetic variation in a mitochondrial marker expected to contain less variation. In the present project the mitochondrial cytochrome b gene was successfully sequenced for 33 of the historic bowhead whale samples. As expected, haplotype and nucleotide diversity based on the cytB was significantly lower rendering this gene a suitable marker for genetic comparisons of bowhead whale stocks. However, cytB sequences did not allow to identify groups of control region based haplotypes.