Phytophthora rubiis a primary causal agent of Phytophthora root rot and wilting of raspberry (Rubus idaeusL.) worldwide. The disease is a major concern for raspberry growers in Canada and USA. To date, no information is available on genomic diversity ofP. rubipopulation from raspberry in Canada. Using a PCR-free library prep with dual-indexing for an Illumina HiSEQX running a 2x150 bp configuration, we generated whole genome sequence data ofP. rubiisolates (n= 25) recovered during 2018 to 2020 from nine fields, four locations and four cultivars of raspberry growing areas of British Columbia, Canada. The assembled genome of 24 isolates ofP. rubiaveraged 8,541 scaffolds, 309× coverage, and 65,960,000 bp. We exploited single nucleotide polymorphisms (SNPs) obtained from whole genome sequence data to analyze the genome structure and genetic diversity of theP.rubiisolates. Low heterozygosity among the 72% of pathogen isolates and standardized index of association revealed that those isolates were clonal. Principal component analysis, discriminant analysis of principal component, and phylogenetic tree revealed thatP. rubiisolates clustered with the raspberry specific cultivars. This study provides novel resources and insight into genome structure, genetic diversity, and reproductive biology ofP rubiisolated from red raspberry. The availability of theP. rubigenomes also provides valuable resources for future comparative genomic and evolutionary studies for oomycetes pathogens.