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A recent increase in flooding events in the northeast has introduced <i>Phytophthora capsici</i>, the cause of Phytophthora Blight, into fields with no prior history of this pathogen. While asexual reproduction is responsible for the rapid escalation of disease within a season, sexual reproduction via oospores allows <i>P. capsici</i> to survive in the soil for many years. To understand the evolutionary dynamics of novel populations of <i>P. capsici</i>, an isolated research farm with no history of <i>P. capsici</i> in Geneva, NY was inoculated with two isolates of opposite mating type (A1 and A2). Approximately, 50 isolates were sampled each year from 2009-2014 from a variety of susceptible plant species. Isolates were genotyped using genotyping-by-sequencing (GBS), which generates single nucleotide polymorphism (SNP) markers from a reduced representation genome, resulting in approximately 100,000 high-quality markers distributed throughout the genome. Shifts in allele and genotype frequencies, and estimates of within year genetic diversity, were used to assess changes in population structure across years. Genome-wide analysis of linkage disequilibrium provided insight into the role of recombination in the population genetics of <i>P. capsici</i>. In addition, these data were used to perform a genome-wide association study, which identified SNPs associated with mating type. Results from the research population will be compared to field populations analyzed using an analogous GBS approach.