Pasteurella multocida is a Gram-negative bacterial pathogen causing economically important diseases in distinct animal species. Complete genome sequences of five P. multocida strains (Pm70, HB03, HN06, 3480, and 36950) isolated from poultry, swine or bovine, were retrieved from the GenBank database and compared with each other, for the first time. The missense mutations generating a dissimilar amino acid in the peptide chain, nonsense mutations, and insertion/deletions in the nucleotide sequence were identified due to the potential change in the protein function. A total of 500 putative mutant proteins were identified, and categorized into 10 groups including cellular compartments such as outer membrane, capsule and fimbria, and processes such as carbohydrate, energy, nucleic acid and amino acid metabolisms, transport, and drug resistance. The majority of the mutant proteins were associated with the outer compartments of the bacterial cell. Various mutations were also detected in the genes related with biosynthetic pathways. The highest and the lowest numbers of mutant proteins belonged to 36950 vs. HN06 and Pm70 vs. HB03 comparisons, respectively. The major impact on the diversification of P. multocida strains was observed to be conferred by the mutations related with pathogenicity. To exhibit the outcomes of the mutations in the peptide chains, three sample amino acid sequences belonging to AfuA, MetB, and d,d-heptose 1,7-bisphosphate phosphatase were aligned, and their phylogenetic relationships were shown. These comprehensive analyses improve the understanding of molecular pathogenicity and host specialization of P. multocida, and would have a contribution to the recombinant vaccine development against this pathogen.