Mannheimia haemolytica is part of the commensal microflora of cattle residing in the upper respiratory tract. In feedlot cattle, M. haemolytica may proliferate and generate a fibrinous pleuropneumonia challenging production economy and animal welfare. Phase shifts in the promotor region of the leukotoxin and an extra repeat of A-tracts have been hypothesized to result in higher virulence (Larsen et al., 2009), however, in the current work, this hypothesis was not confirmed since the same number of repeats was obtained for isolates obtained from both nose and lungs of the same animal during the same outbreak with the same PFGE type (SalI digestion), when 28 strains from 20 animals of three herds were tested. Five of the nose/lung pairs were subsequently analysed by whole genome analysis (IlluminaHiseq2000). Genomes were of sequence type 1 (MLST) with the same leukotoxin gene sequence. SNPs (mapping reads on consensus sequences) between genomes of the same PFGE type were not identified, whereas up to 95 SNPs were found between PFGE types. CRISPR (clustered regularly interspaced short palindromic repeats) analysis with CRISPRFinder identified spacers unique to the published genomes of M. haemolytica or only identified in bacteriophage sequences of phiMhaA1-BAA410 and phiMhaA1-PHL101.Strains from two nose/lung pairs representing two PFGE types had exactly the same CRISPR structure. Strains from one nose/lung pair of a third PFGE profile diverged with respect to the number of CRISPR spacers and one nose/lung pair of a fourth PFGE profile diverged both in direct repeats and CRISPR spacers. Only the CRISPR analysis was able to show differences between clonal isolates obtained from nose and trachea of the same animal during the same outbreak. Factors provoking changes in the CRISR region in the bovine host remain to be identified and investigated further in addition to the biological impact of these observations.