Campylobacter jejuni is a leading cause of gastroenteritis in the world. Widespread use of macrolide and fluoroquinolone antibiotics in animals and humans has resulted in the evolution of antimicrobial resistance (AMR) within Campylobacter, leading to increased costs in healthcare. The objective of this study is to provide insight into the contributions of populations genetics factors including mutation, recombination, and population size and structure on the evolution of virulence and AMR. These processes are investigated to evaluate the potential for local hotspots to contribute disproportionally to antimicrobial resistance in Campylobacter. To test these predictions, 1789 assemblies of Campylobacter jejuni from all across Canada were analyzed to assess rates of recombination and its effect on resulting population structure, and in particular its association antimicrobial resistance alleles. A thorough exploratory analysis has provided limited evidence of positive selection in virulence genes, evidence for one or a few origins of fluoroquinolone resistance as well as high levels of recombination and complex population substructure across the Campylobacter genome.