Ovine footrot is a contagious disease of the feet of sheep. The disease has long been recognised as a problem in the sheep industries of Australia, New Zealand, India and Nepal, and has recently re-emerged in some European countries. Severity of disease ranges from interdigital dermatitis (benign footrot), to underrunning of the horn of the hoof and separation of the horn from the underlying tissue (virulent footrot), leading to lameness and loss of body condition. The principal causative agent of footrot is the bacterium Dichelobacter nodosus, an anaerobic, Gram negative rod, and strains are classified as benign or virulent based on their ability to degrade elastin and their protease thermostability. We now know that these phenotypic differences are the result of a single amino acid substitution in one of the three extracellular proteases secreted by D. nodosus. While the proteases play an important role in disease, and are used for differential diagnosis, our comparative genomic analysis reveals a more deeply entrenched difference between benign and virulent strains. We have sequenced the genomes of 49 isolates, predominantly from Australia and Norway, using Illumina high throughput sequencing. Analysis of conserved regions of these genomes based on read mapping to the reference strain, VCS1703A, identified 9707 sites that were present in all 49 strains but variable amongst the strains. These sites were used to construct a phylogenic tree using the neighbour-joining method. This tree clearly showed that benign and virulent strains could be separated into two distinct clades, and strongly suggests that benign and virulent strains of D. nodosus exist as two separate lineages. These results may lead to the development of new methods for the differential diagnosis of ovine footrot.