Pasteurella multocida is the primary causative agent of a range of economically important diseases in animals, including haemorrhagic septicaemia (HS), a rapidly fatal disease of ungulates. P. multocida strains can be differentiated into five types (A, B, D, E and F) based on the composition of their polysaccharide capsule; HS is caused by capsular type B and E strains. There is very limited information available on the diversity of P. multocida strains that cause HS. In this molecular epidemiological study we investigated the genetic diversity of Pakistani and Thai strains associated with HS. Initially, 24 field isolates and vaccine strains from different regions of Pakistan and Thailand were differentiated by multi-locus sequence typing and pulsed field gel electrophoresis. Based on these analyses, 12 strains were selected for complete genome sequencing. The sequenced strains had draft genomes of between 2,298,035 and 2,410,300 bp in length. Analysis of the genome data identified a core set of 1824 genes that were also shared by the P. multocida strains Pm70, 3480, 36950, HN06 and M1404. A set of 106 unique genes was found to be shared by all HS-associated strains, but absent from Pm70, 3480, 36950 and HN06. Moreover, 59 genes were found to be shared only by Asian B:2 strains. Some regions with high identity to the integrative and conjugative ICEPmu1 element were identified in two Pakistani strains along with a range of other antimicrobial resistance genes. Four different, putative, temperate phages were identified using the PHAST tool. Phylogenetic analysis indicated that there was a correlation between the relatedness of the strains and the country of isolation. Analysis of the 106 genes shared uniquely by HS-associated strains will aid the identification of virulence genes responsible for HS disease and facilitate the development of specific diagnostic tests for HS strains.