Technological advances in genome sequencing have improved our ability to catalog genomic variation and led to an expansion of the scope and scale of genetic studies. Yet, for agronomically important plant pathogens such as the downy-mildews the scale of genetic studies remains limited. This is, in part, due to the difficulties associated with maintaining obligate pathogens, and the logistical constraints involved in the genotyping of these species. To study the genetic variation of two Pseudoperonospora species (P. cubensis and P. humuli), we describe a targeted enrichment (TE) protocol able to genotype isolates using less than 50 ng of mixed pathogen and plant DNA for library preparation. We enriched 830 target genes across 128 samples and identified 2,514 high-quality SNP variants. We detected significant genetic differentiation (p=0.01) between P. cubensis subpopulations from Cucurbita moschata (clade I) and Cucumis sativus (clade II) in Michigan. No evidence of location-based differentiation was detected within the P. cubensis (clade II) subpopulation. A significant effect of location on the genetic variation of the P. humuli subpopulation was detected in the state (p=0.01). Mantel tests found evidence that the genetic distance among P. humuli samples was associated with the physical distance of the hop yards from which the samples were collected (p=0.005). The differences in the distribution of genetic variation of the P. humuli and P. cubensis subpopulations of Michigan suggest differences in the dispersal of these two species. Our TE protocol provides an additional tool for genotyping obligate pathogens and the execution of new genetic studies.