Campylobacter jejuni is one of the leading causes of gastroenteritis in humans. In order to properly interpret surveillance and outbreak data based on whole genome sequencing and to determine whether isolates are related, there must be a baseline understanding C. jejuni genomic diversity. This thesis investigates the genomic diversity and lineage dynamics of a C. jejuni population from 628 live-captured wild raccoons in southern Ontario between 2011 and 2013. To this end, 622 isolates were whole genome sequenced and included for analysis of their core genome and accessory genome. The isolates were grouped by lineage and core genome multilocus sequence typing, pangenome, and a genome wide association study were used to explore and establish the genomic diversity of Campylobacter within this population. Lineages were also examined over time in order to provide context on the microevolution of each lineage and relate time with the lineage diversity. Many raccoons were recaptured over the sampling years, thus lineages were examined across time to examine the C. jejuni status within individual raccoons. The C. jejuni population within the southern Ontario raccoons was diverse. There were 42 total lineages found, of which 20 were raccoon-associated lineages with homogeneous diversity, 6 raccoon-associated lineages had heterogeneous diversity, 8 generalist lineages had homogeneous diversity, and 2 generalist had heterogeneous diversity. Isolates that were identical in the core genome could be quite different in terms of their accessory genome. The lineages, whether heterogeneous or homogeneous, raccoon-associated or generalist, could persist and be found circulating amongst the raccoons over the three sampling years while other lineages were only found during brief periods of time. Within the raccoons, there was high lineage turnover of C. jejuni, re-infection and long-term harbouring of lineages, as well as co-infection of different lineages. The approaches used in this study with whole genome sequencing data should be used in outbreak and epidemiological investigations of C. jejuni.