Pasteurella multocida is a primary pathogen of almost all mammals and birds. P. multocida strains can be differentiated by capsule and LPS type, with strains that produce different surface structures primarily causing disease in different hosts. Little is known about whether pathogenic mechanisms are conserved across diverse strains with different surface structures. To address this, we used transposon directed insertion site sequencing to identify in vivo fitness genes in P. multocida strains VP161 (capsule type A, LPS type L1) and M1404 (capsule type B, LPS type L2) that were recovered from a case of chicken fowl cholera and bison haemorrhagic septicaemia, respectively. P. multocida strain VP161 and M1404 Himar1 mutant libraries were used to induce systemic infections in 6-10-week-old BALB/c mice. Surviving mutants were recovered from the bloodstream, liver and spleen, and used to make TraDIS libraries. The TraDIS libraries were sequenced via Illumina sequencing and data analysed using the Bio-TraDIS toolkit and related scripts. All genes that had a four-fold increase or decrease in reads compared to the input library, and had a q-value < 0.001, were called as fitness-associated. There were 66 fitness-cost and 7 fitness-benefit genes in VP161, and 85 fitness-cost and 7 fitness-benefit genes in M1404. Comparison of fitness-cost genes identified only 33 genes important for fitness in both strains, with 28 genes important only in VP161 and 39 genes important only in M1404. Pathways important for both strains included capsule and LPS biosynthesis, methionine uptake and the TonB-ExbBD system. Ubiquinone biosynthesis and two Na/H+ antiporters were important for fitness only in VP161, and sialic acid uptake and utilisation, a putative iron receptor, catabolite repressor protein and adenylate cyclase were fitness hits only in M1404. Together, these data define the different survival mechanisms in diverse P. multocida strains that produce different surface structures.