Haemorrhagic septicaemia (HS) is an acute fatal septicaemic disease of cattle and buffaloes associated with B:2 (Asian) and E:2 (African) strains of the bacterium Pasteurella multocida. HS is one of the most economically important pasteurelloses, especially in Asia and Africa where it occurs with the highest prevalence. Currently all the genomes (n=21) available on GenBank for strains associated with HS belong to the B:2 serotype. Here we present the first draft genomes of five strains belonging to the E:2 (African) serotype. The time of divergence of these two serotypes was estimated in a Bayesian framework by analyzing the whole-genome single nucleotide polymorphisms. The analysis showed that the divergence between these two lineages was 1.3 million years ago (using an evolutionary rate of 1E-9 substitutions/site/year). These five E:2 genomes were also compared with the genomes of 117 strains of P. multocida (including 21 genomes of B:2 serotype) using Roary to identify those genes that are unique to the HS strains and therefore may be responsible for their pathogenicity. Eleven genes were identified to be unique to the 26 strains belonging to the B:2 and E:2 serotypes. However, when the genomes of the E:2 isolates were excluded from the comparison, the number of genes shared by all strains belonging to the B:2 serotype doubled. These unique genes are predicted to be good targets for a reliable and specific, point-of-care, HS diagnostic test.