Bourret et al. (2022) extracted two loci from twenty-one Phytophthora cactorum genome-sequencing projects for use in a phylogenetic analysis. One locus is ITS rDNA (labeled ITS) and the second is a section of the mitochondrial genome containing portions the "cox2" and "cox1" coding sequences (labeled cox). The sequences are found in two unaligned FASTA (.fasta) files, and each line within is labeled with the BioSample from which the sequences were derived. Sequences were derived by BLASTing a moving window of each locus against data in the sequence read archive corresponding to the listed BioSamples. The 169-isolate, multi-locus alignment used for phylogenetic inference is also included. Alignments are five phylip files (.phy) and a nexus file (.nex) used as the input for IQTREE2. All files contained are standard text files, with extensions describing the different formatting of their contained text.