Genomes that differ significantly from one another are unlikely to have originated from the same parent. It's possible that several pathogen variants are circulating in a given area if people who contracted the disease did so in the same place but their infections had quite different genomes. Information of this nature has been crucial in recent Ebola outbreaks in Africa.
When trying to trace the origins of an outbreak, details like these can be important. How closely related sequencing samples are tells us whether the infectious agent was brought in once and disseminated, or whether it was introduced numerous times, in settings as diverse as a care facility and a whole country.