Phytophthora rubi and P. fragariae are two closely related soil-borne oomycete plant pathogens that exhibit strong morphological and physiological similarities but are specialized to infect different hosts of economic importance, namely, raspberry and strawberry. Here, we report the draft genome sequences of these two Phytophthora species as a first step toward understanding the genomic processes underlying plant host adaptation in these pathogens. Resources in this dataset:Resource Title: Whole Genome Sequences of the Raspberry and Strawberry Pathogens Phytophthora rubi and P. fragariae. File Name: Web Page, url: https://doi.org/10.1094/MPMI-04-17-0081-A Data links from the paper can be found in the related content section of this record.