Plasmodiophora brassicae is an obligate soil-borne pathogen and the (cause of clubroot on canola (Brassica napus)) and other Brassica crops. It is genetically diverse, as exemplified by numerous pathotypes. Whole-genome sequences for collections of P. brassicae from Canada, the USA, and China were developed based on Illumina sequencing technology. The whole genome sequences of 43 P. brassicae of these isolates were compared at the SNP level. The strains from Canada separated into four clades. Strains from the USA and two strains from China were grouped with strains from Canada. Three strains from China formed a separate clade. Strains were mostly grouped based on geographic location and not the pathotype or host. At sites in Ontario and Quebec where the dominant pathotype changed or resistance had broken down, the SNPs differed in about half of the genome between strains before and after the change. This study indicated that rare pathotypes were maintained in the population at very low frequency, maintained through balancing selection, and increased rapidly in response to selection from repeated exposure to host resistance. Micro-manipulation was used to obtain single-spores of the pathogen. The amplification of the DNA of five single spores collected from a single club was attempted to sequence the genome. However, most of the genome was not sequenced in this assessment. Two management methods were assessed: mycorrhizal fungi to protect plants from infection, and grass cover crops to reduce pathogen levels in soil. Some cultivars of cover crops showed promising results in spore reduction in the soil.