[Haemophilus] haemoglobinophilus and the unpublished Bisgaard taxon 35 are associated with respiratory and urogenital tract infections from dogs. The whole genomic sequences were generated for strains CCUG 3714T and CCUG 16472 representing [H.] haemoglobinophilus and taxon 35 by IlluminaHiseq2000. Assembly resulted in 109 contigs for each. The Genome-to-Genome Distance Calculator index 2 was 0.00559 that estimated 58% DNA reassociation, indicating closely related, but separate species related to other members of Pasteurellaceae at genus level. Annotation by 'rapid annotation using subsystem technology' (RAST) surprisingly predicted all three proteins A, B and C of the cytolethal distending proteins (CDT) in both genomes. CDT has previously only been found in [Haemophilus] ducreyi, Aggregatibacter Actinomycetemcomitans, [H.] parasuis and Avibacterium paragallinarum of the Pasteurellaceae. The three CDT proteins A, B and C have been found to form a tripartite complex required for the CDT activity. CDT can induce G2/M cell cycle arrest, chromatin fragmentation, cell distention and nucleus enlargement. CDTA and CDTC probably form a heterodimeric subunit required for the delively of CDTB. CDTB exhibits a DNA-nicking endonuclease activity, and very probably causes DNA damage in intoxicated cells. Outside members of Pasteurellaceae, CDT is best known from members of Escherichia coli, Salmonella typhi, Campylobacter jejuni and Helicobacter hepaticus. The presence of CDT in members of Pasteurellaceae seems unrelated to specific vertebrate hosts, however, final conclusion about the distribution of CDT will have to await whole genome analysis of all members of the Pasteurellaceae. Further work including the development of a PCR test is needed to show if the presence of CDT can be used to separate [H.] haemoglobinophilus and taxon 35 from other canine taxa of Pasteurellaceae including 'Frederiksenia' and Pasteurella sensu stricto.